From yurii.aulchenko at gmail.com  Wed May  1 14:38:12 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 1 May 2013 14:38:12 +0200
Subject: [GenABEL-dev] OmicABEL: DatABEL double format
In-Reply-To: <5177EE38.2050008@karssen.org>
References: <5177EE38.2050008@karssen.org>
Message-ID: <CAHX9t6+uTnyHSUzOvq9WK_JFaSo6whLfP8gEExQJaeS=w=362Q@mail.gmail.com>

I think the conversion would be a quick way out, but I also think that
OmicABEL should allow for FLOAT input - otherwise people will end up
tripling their existing FLOAT-based files storage. And this is really not a
trivial amount of disk space to waste (talking of terabytes).

Diego, do you think this could be something relatively easily solvable?

YA

On Wed, Apr 24, 2013 at 4:37 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Dear list,
>
> I was reading through the OmicABEL tutorial and noted that the DatABEL
> files should be in Double format. By default the GenABEL function
> mach2databel() creates float files.
>
> This means that all existing DatABEL files should be converted to
> double. I guess we should add a "convertType" program to the filevector
> utilities to make life easier for people. Or add a similar R function to
> DatABEL (and update mach2databel()).
>
> Does anybody have an idea if such a conversion from float to double can
> be done quickly? Of course conversion via an intermediate text file is
> also possible, but seems a bit awkward.
>
>
> As an aside, this would probably also fix the problems I ran into while
> trying to make ProbABEL compute everything in doubles (see
>
> http://lists.r-forge.r-project.org/pipermail/genabel-devel/2013-February/000505.html
> ).
>
>
>
> Lennart.
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From fabregat at aices.rwth-aachen.de  Wed May  1 16:24:23 2013
From: fabregat at aices.rwth-aachen.de (Diego Fabregat Traver)
Date: Wed, 01 May 2013 16:24:23 +0200
Subject: [GenABEL-dev] OmicABEL: DatABEL double format
Message-ID: <fb9d8eaf10a013.518141b7@aices.rwth-aachen.de>


Hi everyone,

On 01/05/13, Yurii Aulchenko  <yurii.aulchenko at gmail.com> wrote:

> I think the conversion would be a quick way out, but I also think that OmicABEL should allow for FLOAT input - otherwise people will end up tripling their?existing?FLOAT-based files storage. And this is really not a trivial amount of disk space to waste (talking of terabytes).
> 
> Diego, do you think this could be something relatively easily solvable?

Adding support for multiple input/output datatypes is indeed one of the items in OmicABEL's ToDo list. It will require some changes in the design, possibly trying to build on top of the filevector library. I'm not sure how difficult it will be, especially if we don't want this feature to have a strong impact on performance.

Unfortunately, I'm right now writing my dissertation, which takes up all my time, and cannot work on this issue yet.

Diego

> 
> YA?
> 
> 
> On Wed, Apr 24, 2013 at 4:37 PM, L.C. Karssen <lennart at karssen.org(javascript:main.compose()> wrote:
> 
> 
> > Dear list,
> > 
> > 
> > 
> > I was reading through the OmicABEL tutorial and noted that the DatABEL
> > 
> > files should be in Double format. By default the GenABEL function
> > 
> > mach2databel() creates float files.
> > 
> > 
> > 
> > This means that all existing DatABEL files should be converted to
> > 
> > double. I guess we should add a "convertType" program to the filevector
> > 
> > utilities to make life easier for people. Or add a similar R function to
> > 
> > DatABEL (and update mach2databel()).
> > 
> > 
> > 
> > Does anybody have an idea if such a conversion from float to double can
> > 
> > be done quickly? Of course conversion via an intermediate text file is
> > 
> > also possible, but seems a bit awkward.
> > 
> > 
> > 
> > 
> > 
> > As an aside, this would probably also fix the problems I ran into while
> > 
> > trying to make ProbABEL compute everything in doubles (see
> > 
> > http://lists.r-forge.r-project.org/pipermail/genabel-devel/2013-February/000505.html).
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > Lennart.
> > 
> > --
> > 
> > -----------------------------------------------------------------
> > 
> > L.C. Karssen
> > 
> > Utrecht
> > 
> > The Netherlands
> > 
> > 
> > 
> > lennart at karssen.org <lennart at karssen.org>
> > 
> > http://blog.karssen.org
> > 
> > 
> > 
> > Stuur mij aub geen Word of Powerpoint bestanden!
> > 
> > Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> > 
> > ------------------------------------------------------------------
> > 
> > 
> > 
> > 
> > _______________________________________________
> > 
> > genabel-devel mailing list
> > 
> > genabel-devel at lists.r-forge.r-project.org <genabel-devel at lists.r-forge.r-project.org>
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> > 
> 
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> 
> 
> [?LinkedIn(http://nl.linkedin.com/in/yuriiaulchenko)?]?[ Twitter(http://twitter.com/YuriiAulchenko) ] [ Blog(http://yurii-aulchenko.blogspot.nl/) ]
> 
> 
> 

From yurii.aulchenko at gmail.com  Thu May  2 15:15:05 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 2 May 2013 15:15:05 +0200
Subject: [GenABEL-dev] joining the GenABEL project - what is the procedure?
Message-ID: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>

Dear All,

I have recently received several requests from people who would like to
join to the GenABEL project with their software. Given this is a
community-based project, neither me nor someone else is in a position to
say 'yes' or 'no' - we need to develop some procedure how a software joins
the project.

We have discussed this with Nicola and Lennart during EMGM-2013, and we
think that we do need a technical review as a part of the procedure
(addressing the issues of license, clarity of the code, integration with
other packages, etc.). We also need to think how we do maintenance: the
suggestion would be to request that the author joins the forum and the
list. If we see that a package is not actively maintained (e.g. we can not
reach the maintainer), we should tag such a package as 'orphaned'.

In many respects, we can base our procedure on the procedures developed by
Bioconductor. In our procedures we need to achieve two conflicting goals:
a) we do not want to repel potential contributors by a long list of
technical requirements but at the same time b) in the sake of
maintainability we need the code to comply to some requirements. Probably
we should have 'minimal' and 'complete' requirements with packages clearly
tagged on the web pages.

Let us know what you think. I will initiate a PiratPad document after
having initial response from you.

best regards,
YA
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From kooyman at gmail.com  Thu May  2 20:48:57 2013
From: kooyman at gmail.com (Maarten Kooyman)
Date: Thu, 02 May 2013 20:48:57 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com> <5167B525.6030608@gmail.com>
 <7783033322271622686@unknownmsgid> <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
Message-ID: <5182B519.9070905@gmail.com>

I'm honoured that you continue with my draft! Statistical Genomics  is a 
nice 2 word summary what Genabel is.

Maybe it is a idea to reserve some space in the logo to add the name of 
a sub-project. It is nice to add your own sub-project under one flag 
(logo), but can be a cause of making the thing ugly (like painting a 
name on a national flag).


Maarten

On 04/29/2013 10:15 PM, Yurii Aulchenko wrote:
> Agree.
>
> We have discussed this a bit during EMGM-2013 with Lennart and Nicola, 
> and our suggestion (N, L, please correct me if I am wrong) is to
>
> 1) Pick up Maarten's variant
>
> 2) Replace "project" with "Statistical Genomics" as suggested below
>
> 3) Send this to a professional designer to make it 'nice' (I am 
> willing to pay it unless it is too expensive)
>
> And of cause the logo can evolve later on if we get better ideas :)
>
> Please let us know what you think.
>
> YA
>
> On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen <lennart at karssen.org 
> <mailto:lennart at karssen.org>> wrote:
>
>     Short is better in marketing, so in that sense I agree with
>     Maarten and
>     Yurii. But it should cover what we do in/with the project.
>     What about:
>
>     GenABEL
>     Statistical Genetics
>
>
>     Methodology is too "open", our project is focused on statistical
>     genetics (in all its aspects, from methodology development to
>     implementation and user support, but the core is about analysing
>     genetic
>     data).
>
>
>     Best,
>
>     Lennart.
>
>     On 20/04/13 18:22, Yurii Aulchenko wrote:
>     > Dear All,
>     >
>     > I now tend to agree with Maarten. I have discussed the logos with a
>     > couple of people who know more about design, and it seems that
>     > introducing Greek letters, 0/1 etc may be bad idea - the logo
>     must be
>     > simple. So if we want to deliver extra message it should probably go
>     > to "subheading". The subheading "project" does not carry much
>     info, I
>     > think. I personally like the "statistical toolkit", but I think
>     it may
>     > miss the point that the idea of the project is a bit broader
>     than the
>     > software.
>     >
>     > So, on the top of Maarten's suggestions, what about:
>     >
>     > - methodology project
>     > - open methodology
>     > - methodological toolbox
>     > - methodology
>     > - agile methodology
>     >
>     > YA
>     > ----------------------
>     > Yurii Aulchenko
>     > (sent from mobile device)
>     >
>     > On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com
>     <mailto:kooyman at gmail.com>> wrote:
>     >
>     >> I think a logo must deliver the message in one go. I think it
>     misses is goal if you have to play "where is Waldo?" in a logo:
>     the simpler the better. Adding some greek symbols somewhere
>     increase the "where is Waldo?"-effect.
>     >>
>     >> Maybe it is a idea to replace "project" with "Statistical
>     toolkit" or "statistics project"(or is this plainly rude?)
>     >>
>     >> Maarten
>     >>
>     >> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
>     >>> I think that the greek letters are a good idea although in
>     GenABEL would look very much the same, maybe in project?
>     >>>
>     >>> N.
>     >>>
>     >>> Inviato da iPhone
>     >>>
>     >>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko
>     <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> ha
>     scritto:
>     >>>
>     >>>> What about replacing some letters with Greek ones - this may
>     give some
>     >>>> math flavor?
>     >>>>
>     >>>> YA
>     >>>>
>     >>>> ----------------------
>     >>>> Yurii Aulchenko
>     >>>> (sent from mobile device)
>     >>>>
>     >>>> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org
>     <mailto:lennart at karssen.org>> wrote:
>     >>>>
>     >>>>> Not bad! I really like the way you mixed the G and the DNA.
>     >>>>> Can't we make a combination with Nicola's creation so that
>     we get some
>     >>>>> math in as well? That would nicely integrate two major
>     components of the
>     >>>>> project (only programming would be missing).
>     >>>>>
>     >>>>>
>     >>>>> Lennart
>     >>>>>
>     >>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>     >>>>>> Dear All,
>     >>>>>>
>     >>>>>> I made also a small sketch of a logo. It is pretty raw,
>     colours are
>     >>>>>> wrong , etcetera, etcetera.
>     >>>>>>
>     >>>>>> To quote Nicola:
>     >>>>>> " If you hate it or think it should go in another
>     direction, I'm not
>     >>>>>> touchy so please do tell me. "
>     >>>>>>
>     >>>>>>
>     >>>>>> Cheers,
>     >>>>>>
>     >>>>>> Maarten
>     >>>>>>
>     >>>>>>
>     >>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>     >>>>>>> Dear all,
>     >>>>>>>
>     >>>>>>>
>     >>>>>>> I gave a shot at the logo, it's very simple. Let me know
>     if you like
>     >>>>>>> the general idea, if you'd like to add something or change it.
>     >>>>>>>
>     >>>>>>> As colors I've sticked to those of the website but they can be
>     >>>>>>> changed. Also the pattern for the formulas have some white
>     spaces, but
>     >>>>>>> this is just a quick draft.
>     >>>>>>>
>     >>>>>>> If you hate it or think it should go in another direction,
>     I'm not
>     >>>>>>> touchy so please do tell me.
>     >>>>>>>
>     >>>>>>> Best.
>     >>>>>>>
>     >>>>>>> Nicola
>     >>>>>>
>     >>>>>>> Dear all,
>     >>>>>>>> I really like the proposal, I just to add a few ideas to
>     the discussion.
>     >>>>>>>> I think that there are some important concepts that could
>     be used for
>     >>>>>>>> a logo:
>     >>>>>>>>
>     >>>>>>>> 1) ABEL which is able in the end could be something like
>     a hammer or a
>     >>>>>>>> tool of some sort.
>     >>>>>>>>
>     >>>>>>>> 2) I think that the great thing about the *ABEL project
>     is that it is not
>     >>>>>>>> a single group but it is a network of people and we could
>     rappresent that
>     >>>>>>>> also.
>     >>>>>>>>
>     >>>>>>>> 3) the * in *ABEL could be made by two crossed
>     Chromosomes or something
>     >>>>>>>> else or maybe a DNA strand a tool and something else
>     (Although I do
>     >>>>>>>> realize that it could remind of the comunist party this
>     way :) ).
>     >>>>>>>>
>     >>>>>>>> 4) I do like animals, but I it should be meanigful
>     somehow (although
>     >>>>>>>> Linux
>     >>>>>>>> does have a penguin for some obscure reason).
>     >>>>>>>>
>     >>>>>>>> Best
>     >>>>>>>>
>     >>>>>>>> Nicola
>     >>>>>>>>
>     >>>>>>>>
>     >>>>>>>>
>     >>>>>>>>
>     >>>>>>>>
>     >>>>>>>>
>     >>>>>>>>> Dear Maarten,
>     >>>>>>>>>
>     >>>>>>>>> I have also some irritation about the fact that there is
>     no recognisable
>     >>>>>>>>>> logo on the page. I looks like a complete default page
>     to me: which
>     >>>>>>>>>> gives
>     >>>>>>>>>> me the impression that there is not any on it. Does
>     someone has
>     >>>>>>>>>> graphical
>     >>>>>>>>>> skills to create a nice logo which we can use on the
>     site, posters or
>     >>>>>>>>>> presentations? Having a neat logo, is like wearing a
>     suite: people
>     >>>>>>>>>> think
>     >>>>>>>>>> at
>     >>>>>>>>>> first sight you are more trustworthy,intelligent etc
>     ect. ;)
>     >>>>>>>>> Completely agree and fully support the idea! I even
>     tried to design
>     >>>>>>>>> something myself, but it was SO bad :)
>     >>>>>>>>>
>     >>>>>>>>> Part of the problem is that obvious meaningful symbols (like
>     >>>>>>>>> chromosomes,
>     >>>>>>>>> sigmas and Gaussians) are boring and used for long time.
>     Another part is
>     >>>>>>>>> that we can not just pick say a cute kitty and stop -
>     there should
>     >>>>>>>>> be some
>     >>>>>>>>> meaning to the symbol (or not?).
>     >>>>>>>>>
>     >>>>>>>>> Do we have examples of successful, recognizable logos we
>     like?I like
>     >>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very
>     distinguished.
>     >>>>>>>>>
>     >>>>>>>>> Yurii
>     >>>>>>>>> _______________________________________________
>     >>>>>>>>> genabel-devel mailing list
>     >>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     >>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>>
>     >>>>>>>>>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>     >>>>>>>>
>     >>>>>>>> _______________________________________________
>     >>>>>>>> genabel-devel mailing list
>     >>>>>>>> genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     >>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>>
>     >>>>>>>>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>     >>>>>>>
>     >>>>>>>
>     >>>>>>> _______________________________________________
>     >>>>>>> genabel-devel mailing list
>     >>>>>>> genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     >>>>>>>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>     >>>>>>
>     >>>>>>
>     >>>>>> _______________________________________________
>     >>>>>> genabel-devel mailing list
>     >>>>>> genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     >>>>>>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>     >>>>> --
>     >>>>>
>     -----------------------------------------------------------------
>     >>>>> L.C. Karssen
>     >>>>> Utrecht
>     >>>>> The Netherlands
>     >>>>>
>     >>>>> lennart at karssen.org <mailto:lennart at karssen.org>
>     >>>>> http://blog.karssen.org
>     >>>>>
>     >>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>     >>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>     >>>>>
>     ------------------------------------------------------------------
>     >>>>>
>     >>>>> _______________________________________________
>     >>>>> genabel-devel mailing list
>     >>>>> genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     >>>>>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>     >>>> _______________________________________________
>     >>>> genabel-devel mailing list
>     >>>> genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     >>>>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>     >>> _______________________________________________
>     >>> genabel-devel mailing list
>     >>> genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     >>>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>     >>
>     >> _______________________________________________
>     >> genabel-devel mailing list
>     >> genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     >>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>     > _______________________________________________
>     > genabel-devel mailing list
>     > genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     >
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>     >
>
>     --
>     -----------------------------------------------------------------
>     L.C. Karssen
>     Utrecht
>     The Netherlands
>
>     lennart at karssen.org <mailto:lennart at karssen.org>
>     http://blog.karssen.org
>
>     Stuur mij aub geen Word of Powerpoint bestanden!
>     Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>     ------------------------------------------------------------------
>
>
>     _______________________________________________
>     genabel-devel mailing list
>     genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
>
>
>
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
>
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter 
> <http://twitter.com/YuriiAulchenko> ] [ Blog 
> <http://yurii-aulchenko.blogspot.nl/> ]
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

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From yurii.aulchenko at gmail.com  Thu May  2 21:42:52 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 2 May 2013 21:42:52 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <5182B519.9070905@gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>
 <51671169.5090608@gmail.com> <51671992.9070100@karssen.org>
 <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com>
 <5167B525.6030608@gmail.com> <7783033322271622686@unknownmsgid>
 <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
 <5182B519.9070905@gmail.com>
Message-ID: <CAHX9t6JSV8SAV6y+eiSDiBu96=eEwVH5+v5wEMbJo=scmgC87Q@mail.gmail.com>

Good idea - we should have this in our 'pile of desires' for the designer.

To keep things in the same thread: one more suggestion from one of
the friends is "probably [you] might want to change the blue color to
something lighter, in order to make the G stand out a little bit more
clearly"

YA

On Thu, May 2, 2013 at 8:48 PM, Maarten Kooyman <kooyman at gmail.com> wrote:

>  I'm honoured that you continue with my draft! Statistical Genomics  is a
> nice 2 word summary what Genabel is.
>
> Maybe it is a idea to reserve some space in the logo to add the name of a
> sub-project. It is nice to add your own sub-project under one flag (logo),
> but can be a cause of making the thing ugly (like painting a name on a
> national flag).
>
>
> Maarten
>
> On 04/29/2013 10:15 PM, Yurii Aulchenko wrote:
>
> Agree.
>
>  We have discussed this a bit during EMGM-2013 with Lennart and Nicola,
> and our suggestion (N, L, please correct me if I am wrong) is to
>
>  1) Pick up Maarten's variant
>
>  2) Replace "project" with "Statistical Genomics" as suggested below
>
>  3) Send this to a professional designer to make it 'nice' (I am willing
> to pay it unless it is too expensive)
>
>  And of cause the logo can evolve later on if we get better ideas :)
>
>  Please let us know what you think.
>
>  YA
>
> On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen <lennart at karssen.org>wrote:
>
>> Short is better in marketing, so in that sense I agree with Maarten and
>> Yurii. But it should cover what we do in/with the project.
>> What about:
>>
>> GenABEL
>> Statistical Genetics
>>
>>
>> Methodology is too "open", our project is focused on statistical
>> genetics (in all its aspects, from methodology development to
>> implementation and user support, but the core is about analysing genetic
>> data).
>>
>>
>> Best,
>>
>> Lennart.
>>
>> On 20/04/13 18:22, Yurii Aulchenko wrote:
>> > Dear All,
>> >
>> > I now tend to agree with Maarten. I have discussed the logos with a
>> > couple of people who know more about design, and it seems that
>> > introducing Greek letters, 0/1 etc may be bad idea - the logo must be
>> > simple. So if we want to deliver extra message it should probably go
>> > to "subheading". The subheading "project" does not carry much info, I
>> > think. I personally like the "statistical toolkit", but I think it may
>> > miss the point that the idea of the project is a bit broader than the
>> > software.
>> >
>> > So, on the top of Maarten's suggestions, what about:
>> >
>> > - methodology project
>> > - open methodology
>> > - methodological toolbox
>> > - methodology
>> > - agile methodology
>> >
>> > YA
>> > ----------------------
>> > Yurii Aulchenko
>> > (sent from mobile device)
>> >
>> > On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com> wrote:
>> >
>> >> I think a logo must deliver the message in one go. I think it misses
>> is goal if you have to play "where is Waldo?" in a logo: the simpler the
>> better. Adding some greek symbols somewhere increase the "where is
>> Waldo?"-effect.
>> >>
>> >> Maybe it is a idea to replace "project" with "Statistical toolkit" or
>> "statistics project"(or is this plainly rude?)
>> >>
>> >> Maarten
>> >>
>> >> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
>> >>> I think that the greek letters are a good idea although in GenABEL
>> would look very much the same, maybe in project?
>> >>>
>> >>> N.
>> >>>
>> >>> Inviato da iPhone
>> >>>
>> >>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko <
>> yurii.aulchenko at gmail.com> ha scritto:
>> >>>
>> >>>> What about replacing some letters with Greek ones - this may give
>> some
>> >>>> math flavor?
>> >>>>
>> >>>> YA
>> >>>>
>> >>>> ----------------------
>> >>>> Yurii Aulchenko
>> >>>> (sent from mobile device)
>> >>>>
>> >>>> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org>
>> wrote:
>> >>>>
>> >>>>> Not bad! I really like the way you mixed the G and the DNA.
>> >>>>> Can't we make a combination with Nicola's creation so that we get
>> some
>> >>>>> math in as well? That would nicely integrate two major components
>> of the
>> >>>>> project (only programming would be missing).
>> >>>>>
>> >>>>>
>> >>>>> Lennart
>> >>>>>
>> >>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>> >>>>>> Dear All,
>> >>>>>>
>> >>>>>> I made also a small sketch of a logo. It is pretty raw, colours are
>> >>>>>> wrong , etcetera, etcetera.
>> >>>>>>
>> >>>>>> To quote Nicola:
>> >>>>>> " If you hate it or think it should go in another direction, I'm
>> not
>> >>>>>> touchy so please do tell me. "
>> >>>>>>
>> >>>>>>
>> >>>>>> Cheers,
>> >>>>>>
>> >>>>>> Maarten
>> >>>>>>
>> >>>>>>
>> >>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>> >>>>>>> Dear all,
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> I gave a shot at the logo, it's very simple. Let me know if you
>> like
>> >>>>>>> the general idea, if you'd like to add something or change it.
>> >>>>>>>
>> >>>>>>> As colors I've sticked to those of the website but they can be
>> >>>>>>> changed. Also the pattern for the formulas have some white
>> spaces, but
>> >>>>>>> this is just a quick draft.
>> >>>>>>>
>> >>>>>>> If you hate it or think it should go in another direction, I'm not
>> >>>>>>> touchy so please do tell me.
>> >>>>>>>
>> >>>>>>> Best.
>> >>>>>>>
>> >>>>>>> Nicola
>> >>>>>>
>> >>>>>>> Dear all,
>> >>>>>>>> I really like the proposal, I just to add a few ideas to the
>> discussion.
>> >>>>>>>> I think that there are some important concepts that could be
>> used for
>> >>>>>>>> a logo:
>> >>>>>>>>
>> >>>>>>>> 1) ABEL which is able in the end could be something like a
>> hammer or a
>> >>>>>>>> tool of some sort.
>> >>>>>>>>
>> >>>>>>>> 2) I think that the great thing about the *ABEL project is that
>> it is not
>> >>>>>>>> a single group but it is a network of people and we could
>> rappresent that
>> >>>>>>>> also.
>> >>>>>>>>
>> >>>>>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or
>> something
>> >>>>>>>> else or maybe a DNA strand a tool and something else (Although I
>> do
>> >>>>>>>> realize that it could remind of the comunist party this way :) ).
>> >>>>>>>>
>> >>>>>>>> 4) I do like animals, but I it should be meanigful somehow
>> (although
>> >>>>>>>> Linux
>> >>>>>>>> does have a penguin for some obscure reason).
>> >>>>>>>>
>> >>>>>>>> Best
>> >>>>>>>>
>> >>>>>>>> Nicola
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>> Dear Maarten,
>> >>>>>>>>>
>> >>>>>>>>> I have also some irritation about the fact that there is no
>> recognisable
>> >>>>>>>>>> logo on the page. I looks like a complete default page to me:
>> which
>> >>>>>>>>>> gives
>> >>>>>>>>>> me the impression that there is not any on it. Does someone has
>> >>>>>>>>>> graphical
>> >>>>>>>>>> skills to create a nice logo which we can use on the site,
>> posters or
>> >>>>>>>>>> presentations? Having a neat logo, is like wearing a suite:
>> people
>> >>>>>>>>>> think
>> >>>>>>>>>> at
>> >>>>>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>> >>>>>>>>> Completely agree and fully support the idea! I even tried to
>> design
>> >>>>>>>>> something myself, but it was SO bad :)
>> >>>>>>>>>
>> >>>>>>>>> Part of the problem is that obvious meaningful symbols (like
>> >>>>>>>>> chromosomes,
>> >>>>>>>>> sigmas and Gaussians) are boring and used for long time.
>> Another part is
>> >>>>>>>>> that we can not just pick say a cute kitty and stop - there
>> should
>> >>>>>>>>> be some
>> >>>>>>>>> meaning to the symbol (or not?).
>> >>>>>>>>>
>> >>>>>>>>> Do we have examples of successful, recognizable logos we like?I
>> like
>> >>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very
>> distinguished.
>> >>>>>>>>>
>> >>>>>>>>> Yurii
>> >>>>>>>>> _______________________________________________
>> >>>>>>>>> genabel-devel mailing list
>> >>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>> >>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>> >>>>>>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>>>>>>>
>> >>>>>>>> _______________________________________________
>> >>>>>>>> genabel-devel mailing list
>> >>>>>>>> genabel-devel at lists.r-forge.r-project.org
>> >>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>> >>>>>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> _______________________________________________
>> >>>>>>> genabel-devel mailing list
>> >>>>>>> genabel-devel at lists.r-forge.r-project.org
>> >>>>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>>>>>
>> >>>>>>
>> >>>>>> _______________________________________________
>> >>>>>> genabel-devel mailing list
>> >>>>>> genabel-devel at lists.r-forge.r-project.org
>> >>>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>>>> --
>> >>>>> -----------------------------------------------------------------
>> >>>>> L.C. Karssen
>> >>>>> Utrecht
>> >>>>> The Netherlands
>> >>>>>
>> >>>>> lennart at karssen.org
>> >>>>> http://blog.karssen.org
>> >>>>>
>> >>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>> >>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>> >>>>> ------------------------------------------------------------------
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> genabel-devel mailing list
>> >>>>> genabel-devel at lists.r-forge.r-project.org
>> >>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>>> _______________________________________________
>> >>>> genabel-devel mailing list
>> >>>> genabel-devel at lists.r-forge.r-project.org
>> >>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>> _______________________________________________
>> >>> genabel-devel mailing list
>> >>> genabel-devel at lists.r-forge.r-project.org
>> >>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>
>> >> _______________________________________________
>> >> genabel-devel mailing list
>> >> genabel-devel at lists.r-forge.r-project.org
>> >>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> > _______________________________________________
>> > genabel-devel mailing list
>> > genabel-devel at lists.r-forge.r-project.org
>> >
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >
>>
>> --
>> -----------------------------------------------------------------
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>>
>> lennart at karssen.org
>> http://blog.karssen.org
>>
>> Stuur mij aub geen Word of Powerpoint bestanden!
>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>> ------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>
>
>
>  --
> -----------------------------------------------------
> Yurii S. Aulchenko
>
>  [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter<http://twitter.com/YuriiAulchenko>] [
> Blog <http://yurii-aulchenko.blogspot.nl/> ]
>
>
> _______________________________________________
> genabel-devel mailing listgenabel-devel at lists.r-forge.r-project.orghttps://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
>
>


-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From nicola.pirastu at burlo.trieste.it  Fri May  3 12:02:46 2013
From: nicola.pirastu at burlo.trieste.it (Nicola Pirastu)
Date: Fri, 3 May 2013 12:02:46 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <CAHX9t6JSV8SAV6y+eiSDiBu96=eEwVH5+v5wEMbJo=scmgC87Q@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
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 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com> <5167B525.6030608@gmail.com>
 <7783033322271622686@unknownmsgid> <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
 <5182B519.9070905@gmail.com>
 <CAHX9t6JSV8SAV6y+eiSDiBu96=eEwVH5+v5wEMbJo=scmgC87Q@mail.gmail.com>
Message-ID: <7301A11D-E1CA-4852-8488-34513253C722@burlo.trieste.it>

Hi everyone,


Il giorno 02/mag/2013, alle ore 21:42, Yurii Aulchenko <yurii.aulchenko at gmail.com<mailto:yurii.aulchenko at gmail.com>> ha scritto:

Good idea - we should have this in our 'pile of desires' for the designer.

To keep things in the same thread: one more suggestion from one of the friends is "probably [you] might want to change the blue color to something lighter, in order to make the G stand out a little bit more clearly"


I think that for colors if you go to a professional he could propose some "good" combinations.
For some reason I don't quite get ,I associate GenABEL to blue colors but we can always decide to opt to another. Also if I really have to be honest I would avoid black.

To give you some inspiration, take a look at this image which summarizes famous logos by color. Note that actually some top brands like google microsoft and ebay are multiple colors, which could be an option as well since we have so many different subprojects.

http://blog.logomyway.com/wp-content/uploads/2012/05/Logo-Wheel.jpg

Nicola



YA

On Thu, May 2, 2013 at 8:48 PM, Maarten Kooyman <kooyman at gmail.com<mailto:kooyman at gmail.com>> wrote:
I'm honoured that you continue with my draft! Statistical Genomics  is a nice 2 word summary what Genabel is.

Maybe it is a idea to reserve some space in the logo to add the name of a sub-project. It is nice to add your own sub-project under one flag (logo), but can be a cause of making the thing ugly (like painting a name on a national flag).


Maarten

On 04/29/2013 10:15 PM, Yurii Aulchenko wrote:
Agree.

We have discussed this a bit during EMGM-2013 with Lennart and Nicola, and our suggestion (N, L, please correct me if I am wrong) is to

1) Pick up Maarten's variant

2) Replace "project" with "Statistical Genomics" as suggested below

3) Send this to a professional designer to make it 'nice' (I am willing to pay it unless it is too expensive)

And of cause the logo can evolve later on if we get better ideas :)

Please let us know what you think.

YA

On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen <lennart at karssen.org<mailto:lennart at karssen.org>> wrote:
Short is better in marketing, so in that sense I agree with Maarten and
Yurii. But it should cover what we do in/with the project.
What about:

GenABEL
Statistical Genetics


Methodology is too "open", our project is focused on statistical
genetics (in all its aspects, from methodology development to
implementation and user support, but the core is about analysing genetic
data).


Best,

Lennart.

On 20/04/13 18:22, Yurii Aulchenko wrote:
> Dear All,
>
> I now tend to agree with Maarten. I have discussed the logos with a
> couple of people who know more about design, and it seems that
> introducing Greek letters, 0/1 etc may be bad idea - the logo must be
> simple. So if we want to deliver extra message it should probably go
> to "subheading". The subheading "project" does not carry much info, I
> think. I personally like the "statistical toolkit", but I think it may
> miss the point that the idea of the project is a bit broader than the
> software.
>
> So, on the top of Maarten's suggestions, what about:
>
> - methodology project
> - open methodology
> - methodological toolbox
> - methodology
> - agile methodology
>
> YA
> ----------------------
> Yurii Aulchenko
> (sent from mobile device)
>
> On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com<mailto:kooyman at gmail.com>> wrote:
>
>> I think a logo must deliver the message in one go. I think it misses is goal if you have to play "where is Waldo?" in a logo: the simpler the better. Adding some greek symbols somewhere increase the "where is Waldo?"-effect.
>>
>> Maybe it is a idea to replace "project" with "Statistical toolkit" or "statistics project"(or is this plainly rude?)
>>
>> Maarten
>>
>> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
>>> I think that the greek letters are a good idea although in GenABEL would look very much the same, maybe in project?
>>>
>>> N.
>>>
>>> Inviato da iPhone
>>>
>>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko <yurii.aulchenko at gmail.com<mailto:yurii.aulchenko at gmail.com>> ha scritto:
>>>
>>>> What about replacing some letters with Greek ones - this may give some
>>>> math flavor?
>>>>
>>>> YA
>>>>
>>>> ----------------------
>>>> Yurii Aulchenko
>>>> (sent from mobile device)
>>>>
>>>> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org<mailto:lennart at karssen.org>> wrote:
>>>>
>>>>> Not bad! I really like the way you mixed the G and the DNA.
>>>>> Can't we make a combination with Nicola's creation so that we get some
>>>>> math in as well? That would nicely integrate two major components of the
>>>>> project (only programming would be missing).
>>>>>
>>>>>
>>>>> Lennart
>>>>>
>>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>>>>>> Dear All,
>>>>>>
>>>>>> I made also a small sketch of a logo. It is pretty raw, colours are
>>>>>> wrong , etcetera, etcetera.
>>>>>>
>>>>>> To quote Nicola:
>>>>>> " If you hate it or think it should go in another direction, I'm not
>>>>>> touchy so please do tell me. "
>>>>>>
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Maarten
>>>>>>
>>>>>>
>>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>>>>>>> Dear all,
>>>>>>>
>>>>>>>
>>>>>>> I gave a shot at the logo, it's very simple. Let me know if you like
>>>>>>> the general idea, if you'd like to add something or change it.
>>>>>>>
>>>>>>> As colors I've sticked to those of the website but they can be
>>>>>>> changed. Also the pattern for the formulas have some white spaces, but
>>>>>>> this is just a quick draft.
>>>>>>>
>>>>>>> If you hate it or think it should go in another direction, I'm not
>>>>>>> touchy so please do tell me.
>>>>>>>
>>>>>>> Best.
>>>>>>>
>>>>>>> Nicola
>>>>>>
>>>>>>> Dear all,
>>>>>>>> I really like the proposal, I just to add a few ideas to the discussion.
>>>>>>>> I think that there are some important concepts that could be used for
>>>>>>>> a logo:
>>>>>>>>
>>>>>>>> 1) ABEL which is able in the end could be something like a hammer or a
>>>>>>>> tool of some sort.
>>>>>>>>
>>>>>>>> 2) I think that the great thing about the *ABEL project is that it is not
>>>>>>>> a single group but it is a network of people and we could rappresent that
>>>>>>>> also.
>>>>>>>>
>>>>>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
>>>>>>>> else or maybe a DNA strand a tool and something else (Although I do
>>>>>>>> realize that it could remind of the comunist party this way :) ).
>>>>>>>>
>>>>>>>> 4) I do like animals, but I it should be meanigful somehow (although
>>>>>>>> Linux
>>>>>>>> does have a penguin for some obscure reason).
>>>>>>>>
>>>>>>>> Best
>>>>>>>>
>>>>>>>> Nicola
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Dear Maarten,
>>>>>>>>>
>>>>>>>>> I have also some irritation about the fact that there is no recognisable
>>>>>>>>>> logo on the page. I looks like a complete default page to me: which
>>>>>>>>>> gives
>>>>>>>>>> me the impression that there is not any on it. Does someone has
>>>>>>>>>> graphical
>>>>>>>>>> skills to create a nice logo which we can use on the site, posters or
>>>>>>>>>> presentations? Having a neat logo, is like wearing a suite: people
>>>>>>>>>> think
>>>>>>>>>> at
>>>>>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>>>>>>> Completely agree and fully support the idea! I even tried to design
>>>>>>>>> something myself, but it was SO bad :)
>>>>>>>>>
>>>>>>>>> Part of the problem is that obvious meaningful symbols (like
>>>>>>>>> chromosomes,
>>>>>>>>> sigmas and Gaussians) are boring and used for long time. Another part is
>>>>>>>>> that we can not just pick say a cute kitty and stop - there should
>>>>>>>>> be some
>>>>>>>>> meaning to the symbol (or not?).
>>>>>>>>>
>>>>>>>>> Do we have examples of successful, recognizable logos we like?I like
>>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>>>>>>>>
>>>>>>>>> Yurii
>>>>>>>>> _______________________________________________
>>>>>>>>> genabel-devel mailing list
>>>>>>>>> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>>
>>>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> genabel-devel mailing list
>>>>>>>> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>>
>>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> genabel-devel mailing list
>>>>>>> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> genabel-devel mailing list
>>>>>> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>> --
>>>>> -----------------------------------------------------------------
>>>>> L.C. Karssen
>>>>> Utrecht
>>>>> The Netherlands
>>>>>
>>>>> lennart at karssen.org<mailto:lennart at karssen.org>
>>>>> http://blog.karssen.org<http://blog.karssen.org/>
>>>>>
>>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>>> ------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>

--
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org<mailto:lennart at karssen.org>
http://blog.karssen.org<http://blog.karssen.org/>

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------


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genabel-devel mailing list
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https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel



--
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn<http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter<http://twitter.com/YuriiAulchenko> ] [ Blog<http://yurii-aulchenko.blogspot.nl/> ]



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--
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn<http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter<http://twitter.com/YuriiAulchenko> ] [ Blog<http://yurii-aulchenko.blogspot.nl/> ]
_______________________________________________
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From lennart at karssen.org  Fri May  3 13:30:23 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 03 May 2013 13:30:23 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <7301A11D-E1CA-4852-8488-34513253C722@burlo.trieste.it>
References: <515446DC.6040602@karssen.org>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com> <5167B525.6030608@gmail.com>
 <7783033322271622686@unknownmsgid> <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
 <5182B519.9070905@gmail.com>
 <CAHX9t6JSV8SAV6y+eiSDiBu96=eEwVH5+v5wEMbJo=scmgC87Q@mail.gmail.com>
 <7301A11D-E1CA-4852-8488-34513253C722@burlo.trieste.it>
Message-ID: <51839FCF.6040306@karssen.org>

Hi all,

Looking at the logo wheel Nicola linked to it seems that the blue logos
are mostly IT (and the other way around: non-blue logos are mostly
non-IT. Would that be a coincidence?


Lennart.

On 03/05/13 12:02, Nicola Pirastu wrote:
> Hi everyone,
> 
> 
> Il giorno 02/mag/2013, alle ore 21:42, Yurii Aulchenko
> <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> ha scritto:
> 
>> Good idea - we should have this in our 'pile of desires' for the
>> designer.
>>
>> To keep things in the same thread: one more suggestion from one of
>> the friends is "probably [you] might want to change the blue color to
>> something lighter, in order to make the G stand out a little bit more
>> clearly"
>>
> 
> I think that for colors if you go to a professional he could propose
> some "good" combinations. 
> For some reason I don't quite get ,I associate GenABEL to blue colors
> but we can always decide to opt to another. Also if I really have to be
> honest I would avoid black.
> 
> To give you some inspiration, take a look at this image which summarizes
> famous logos by color. Note that actually some top brands like google
> microsoft and ebay are multiple colors, which could be an option as well
> since we have so many different subprojects.
> 
> http://blog.logomyway.com/wp-content/uploads/2012/05/Logo-Wheel.jpg
> 
> Nicola
> 
> 
> 
>> YA
>>
>> On Thu, May 2, 2013 at 8:48 PM, Maarten Kooyman <kooyman at gmail.com
>> <mailto:kooyman at gmail.com>> wrote:
>>
>>     I'm honoured that you continue with my draft! Statistical
>>     Genomics  is a nice 2 word summary what Genabel is.
>>
>>     Maybe it is a idea to reserve some space in the logo to add the
>>     name of a sub-project. It is nice to add your own sub-project
>>     under one flag (logo), but can be a cause of making the thing ugly
>>     (like painting a name on a national flag).
>>
>>
>>     Maarten
>>
>>     On 04/29/2013 10:15 PM, Yurii Aulchenko wrote:
>>>     Agree.
>>>
>>>     We have discussed this a bit during EMGM-2013 with Lennart and
>>>     Nicola, and our suggestion (N, L, please correct me if I am
>>>     wrong) is to 
>>>
>>>     1) Pick up Maarten's variant 
>>>
>>>     2) Replace "project" with "Statistical Genomics" as suggested below
>>>
>>>     3) Send this to a professional designer to make it 'nice' (I am
>>>     willing to pay it unless it is too expensive)
>>>
>>>     And of cause the logo can evolve later on if we get better ideas :)
>>>
>>>     Please let us know what you think. 
>>>
>>>     YA
>>>
>>>     On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen
>>>     <lennart at karssen.org <mailto:lennart at karssen.org>> wrote:
>>>
>>>         Short is better in marketing, so in that sense I agree with
>>>         Maarten and
>>>         Yurii. But it should cover what we do in/with the project.
>>>         What about:
>>>
>>>         GenABEL
>>>         Statistical Genetics
>>>
>>>
>>>         Methodology is too "open", our project is focused on statistical
>>>         genetics (in all its aspects, from methodology development to
>>>         implementation and user support, but the core is about
>>>         analysing genetic
>>>         data).
>>>
>>>
>>>         Best,
>>>
>>>         Lennart.
>>>
>>>         On 20/04/13 18:22, Yurii Aulchenko wrote:
>>>         > Dear All,
>>>         >
>>>         > I now tend to agree with Maarten. I have discussed the
>>>         logos with a
>>>         > couple of people who know more about design, and it seems that
>>>         > introducing Greek letters, 0/1 etc may be bad idea - the
>>>         logo must be
>>>         > simple. So if we want to deliver extra message it should
>>>         probably go
>>>         > to "subheading". The subheading "project" does not carry
>>>         much info, I
>>>         > think. I personally like the "statistical toolkit", but I
>>>         think it may
>>>         > miss the point that the idea of the project is a bit
>>>         broader than the
>>>         > software.
>>>         >
>>>         > So, on the top of Maarten's suggestions, what about:
>>>         >
>>>         > - methodology project
>>>         > - open methodology
>>>         > - methodological toolbox
>>>         > - methodology
>>>         > - agile methodology
>>>         >
>>>         > YA
>>>         > ----------------------
>>>         > Yurii Aulchenko
>>>         > (sent from mobile device)
>>>         >
>>>         > On 12 Apr 2013, at 09:18, Maarten Kooyman
>>>         <kooyman at gmail.com <mailto:kooyman at gmail.com>> wrote:
>>>         >
>>>         >> I think a logo must deliver the message in one go. I think
>>>         it misses is goal if you have to play "where is Waldo?" in a
>>>         logo: the simpler the better. Adding some greek symbols
>>>         somewhere increase the "where is Waldo?"-effect.
>>>         >>
>>>         >> Maybe it is a idea to replace "project" with "Statistical
>>>         toolkit" or "statistics project"(or is this plainly rude?)
>>>         >>
>>>         >> Maarten
>>>         >>
>>>         >> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
>>>         >>> I think that the greek letters are a good idea although
>>>         in GenABEL would look very much the same, maybe in project?
>>>         >>>
>>>         >>> N.
>>>         >>>
>>>         >>> Inviato da iPhone
>>>         >>>
>>>         >>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko
>>>         <yurii.aulchenko at gmail.com
>>>         <mailto:yurii.aulchenko at gmail.com>> ha scritto:
>>>         >>>
>>>         >>>> What about replacing some letters with Greek ones - this
>>>         may give some
>>>         >>>> math flavor?
>>>         >>>>
>>>         >>>> YA
>>>         >>>>
>>>         >>>> ----------------------
>>>         >>>> Yurii Aulchenko
>>>         >>>> (sent from mobile device)
>>>         >>>>
>>>         >>>> On 11 Apr 2013, at 22:14, "L.C. Karssen"
>>>         <lennart at karssen.org <mailto:lennart at karssen.org>> wrote:
>>>         >>>>
>>>         >>>>> Not bad! I really like the way you mixed the G and the DNA.
>>>         >>>>> Can't we make a combination with Nicola's creation so
>>>         that we get some
>>>         >>>>> math in as well? That would nicely integrate two major
>>>         components of the
>>>         >>>>> project (only programming would be missing).
>>>         >>>>>
>>>         >>>>>
>>>         >>>>> Lennart
>>>         >>>>>
>>>         >>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>>>         >>>>>> Dear All,
>>>         >>>>>>
>>>         >>>>>> I made also a small sketch of a logo. It is pretty
>>>         raw, colours are
>>>         >>>>>> wrong , etcetera, etcetera.
>>>         >>>>>>
>>>         >>>>>> To quote Nicola:
>>>         >>>>>> " If you hate it or think it should go in another
>>>         direction, I'm not
>>>         >>>>>> touchy so please do tell me. "
>>>         >>>>>>
>>>         >>>>>>
>>>         >>>>>> Cheers,
>>>         >>>>>>
>>>         >>>>>> Maarten
>>>         >>>>>>
>>>         >>>>>>
>>>         >>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>>>         >>>>>>> Dear all,
>>>         >>>>>>>
>>>         >>>>>>>
>>>         >>>>>>> I gave a shot at the logo, it's very simple. Let me
>>>         know if you like
>>>         >>>>>>> the general idea, if you'd like to add something or
>>>         change it.
>>>         >>>>>>>
>>>         >>>>>>> As colors I've sticked to those of the website but
>>>         they can be
>>>         >>>>>>> changed. Also the pattern for the formulas have some
>>>         white spaces, but
>>>         >>>>>>> this is just a quick draft.
>>>         >>>>>>>
>>>         >>>>>>> If you hate it or think it should go in another
>>>         direction, I'm not
>>>         >>>>>>> touchy so please do tell me.
>>>         >>>>>>>
>>>         >>>>>>> Best.
>>>         >>>>>>>
>>>         >>>>>>> Nicola
>>>         >>>>>>
>>>         >>>>>>> Dear all,
>>>         >>>>>>>> I really like the proposal, I just to add a few
>>>         ideas to the discussion.
>>>         >>>>>>>> I think that there are some important concepts that
>>>         could be used for
>>>         >>>>>>>> a logo:
>>>         >>>>>>>>
>>>         >>>>>>>> 1) ABEL which is able in the end could be something
>>>         like a hammer or a
>>>         >>>>>>>> tool of some sort.
>>>         >>>>>>>>
>>>         >>>>>>>> 2) I think that the great thing about the *ABEL
>>>         project is that it is not
>>>         >>>>>>>> a single group but it is a network of people and we
>>>         could rappresent that
>>>         >>>>>>>> also.
>>>         >>>>>>>>
>>>         >>>>>>>> 3) the * in *ABEL could be made by two crossed
>>>         Chromosomes or something
>>>         >>>>>>>> else or maybe a DNA strand a tool and something else
>>>         (Although I do
>>>         >>>>>>>> realize that it could remind of the comunist party
>>>         this way :) ).
>>>         >>>>>>>>
>>>         >>>>>>>> 4) I do like animals, but I it should be meanigful
>>>         somehow (although
>>>         >>>>>>>> Linux
>>>         >>>>>>>> does have a penguin for some obscure reason).
>>>         >>>>>>>>
>>>         >>>>>>>> Best
>>>         >>>>>>>>
>>>         >>>>>>>> Nicola
>>>         >>>>>>>>
>>>         >>>>>>>>
>>>         >>>>>>>>
>>>         >>>>>>>>
>>>         >>>>>>>>
>>>         >>>>>>>>
>>>         >>>>>>>>> Dear Maarten,
>>>         >>>>>>>>>
>>>         >>>>>>>>> I have also some irritation about the fact that
>>>         there is no recognisable
>>>         >>>>>>>>>> logo on the page. I looks like a complete default
>>>         page to me: which
>>>         >>>>>>>>>> gives
>>>         >>>>>>>>>> me the impression that there is not any on it.
>>>         Does someone has
>>>         >>>>>>>>>> graphical
>>>         >>>>>>>>>> skills to create a nice logo which we can use on
>>>         the site, posters or
>>>         >>>>>>>>>> presentations? Having a neat logo, is like wearing
>>>         a suite: people
>>>         >>>>>>>>>> think
>>>         >>>>>>>>>> at
>>>         >>>>>>>>>> first sight you are more trustworthy,intelligent
>>>         etc ect. ;)
>>>         >>>>>>>>> Completely agree and fully support the idea! I even
>>>         tried to design
>>>         >>>>>>>>> something myself, but it was SO bad :)
>>>         >>>>>>>>>
>>>         >>>>>>>>> Part of the problem is that obvious meaningful
>>>         symbols (like
>>>         >>>>>>>>> chromosomes,
>>>         >>>>>>>>> sigmas and Gaussians) are boring and used for long
>>>         time. Another part is
>>>         >>>>>>>>> that we can not just pick say a cute kitty and stop
>>>         - there should
>>>         >>>>>>>>> be some
>>>         >>>>>>>>> meaning to the symbol (or not?).
>>>         >>>>>>>>>
>>>         >>>>>>>>> Do we have examples of successful, recognizable
>>>         logos we like?I like
>>>         >>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are
>>>         very distinguished.
>>>         >>>>>>>>>
>>>         >>>>>>>>> Yurii
>>>         >>>>>>>>> _______________________________________________
>>>         >>>>>>>>> genabel-devel mailing list
>>>         >>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         >>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>>
>>>         >>>>>>>>>
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>         >>>>>>>>
>>>         >>>>>>>> _______________________________________________
>>>         >>>>>>>> genabel-devel mailing list
>>>         >>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         >>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>>
>>>         >>>>>>>>
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>         >>>>>>>
>>>         >>>>>>>
>>>         >>>>>>> _______________________________________________
>>>         >>>>>>> genabel-devel mailing list
>>>         >>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         >>>>>>>
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>         >>>>>>
>>>         >>>>>>
>>>         >>>>>> _______________________________________________
>>>         >>>>>> genabel-devel mailing list
>>>         >>>>>> genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         >>>>>>
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>         >>>>> --
>>>         >>>>>
>>>         -----------------------------------------------------------------
>>>         >>>>> L.C. Karssen
>>>         >>>>> Utrecht
>>>         >>>>> The Netherlands
>>>         >>>>>
>>>         >>>>> lennart at karssen.org <mailto:lennart at karssen.org>
>>>         >>>>> http://blog.karssen.org <http://blog.karssen.org/>
>>>         >>>>>
>>>         >>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>>         >>>>> Zie
>>>         http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>         >>>>>
>>>         ------------------------------------------------------------------
>>>         >>>>>
>>>         >>>>> _______________________________________________
>>>         >>>>> genabel-devel mailing list
>>>         >>>>> genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         >>>>>
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>         >>>> _______________________________________________
>>>         >>>> genabel-devel mailing list
>>>         >>>> genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         >>>>
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>         >>> _______________________________________________
>>>         >>> genabel-devel mailing list
>>>         >>> genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         >>>
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>         >>
>>>         >> _______________________________________________
>>>         >> genabel-devel mailing list
>>>         >> genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         >>
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>         > _______________________________________________
>>>         > genabel-devel mailing list
>>>         > genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         >
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>         >
>>>
>>>         --
>>>         -----------------------------------------------------------------
>>>         L.C. Karssen
>>>         Utrecht
>>>         The Netherlands
>>>
>>>         lennart at karssen.org <mailto:lennart at karssen.org>
>>>         http://blog.karssen.org <http://blog.karssen.org/>
>>>
>>>         Stuur mij aub geen Word of Powerpoint bestanden!
>>>         Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>         ------------------------------------------------------------------
>>>
>>>
>>>         _______________________________________________
>>>         genabel-devel mailing list
>>>         genabel-devel at lists.r-forge.r-project.org
>>>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>
>>>
>>>
>>>
>>>     -- 
>>>     -----------------------------------------------------
>>>     Yurii S. Aulchenko
>>>
>>>     [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
>>>     <http://twitter.com/YuriiAulchenko> ] [ Blog
>>>     <http://yurii-aulchenko.blogspot.nl/> ]
>>>
>>>
>>>     _______________________________________________
>>>     genabel-devel mailing list
>>>     genabel-devel at lists.r-forge.r-project.org <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>>
>>
>>
>> -- 
>> -----------------------------------------------------
>> Yurii S. Aulchenko
>>
>> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
>> <http://twitter.com/YuriiAulchenko> ] [ Blog
>> <http://yurii-aulchenko.blogspot.nl/> ]
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute
> nel messaggio o nei suoi allegati. Se non siete i destinatari indicati
> nel messaggio, o responsabili per la sua consegna alla persona, o se
> avete ricevuto il messaggio per errore, siete pregati di non
> trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a
> cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY
> NOTICE Confidential information may be contained in this message or in
> its attachments. If you are not the addressee indicated in this message,
> or responsible for message delivering to that person, or if you have
> received this message in error, you may not transcribe, copy or deliver
> this message to anyone. In that case, you should delete this message and
> its attachments. Thank you.
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
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From lennart at karssen.org  Tue May 14 00:07:35 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Tue, 14 May 2013 00:07:35 +0200
Subject: [GenABEL-dev] joining the GenABEL project - what is the
	procedure?
In-Reply-To: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
References: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
Message-ID: <51916427.8020307@karssen.org>

Dear all,

It's been a while but this mail was still on my todo list. I agree with
Yurii that we should start establishing procedures for projects wanting
to join the GenABEL project umbrella. Software lifecycle management is
too often overlooked when developing a package and we don't want to
'degrade' the GenABEL project brand name by including packages that are
not maintained anymore after the initial paper is published. Or, another
argument I've come across: we make it open source so everyone can
contribute to it (and therefore it will 'somehow' be maintained without
us putting more effort into it). That's not how it works. The software
ecosystem in which a package lives is dynamic and a package should adapt
to that.

As Yurii wrote we discussed this at the EMGM conference and agreed that
code review should be part of it. This neatly ties into the discussion
we had on thils list some time ago about coding standards. This does not
mean we force everybody to use four spaces instead of eight when
indenting code, but more serious stuff like variables named "a" or "df"
are not helpful when someone wants to contribute or take over
maintenance of the package.

I've just committed the draft document of the coding standards to the
www folder of the SVN repo (rev. 1215). It's a (plain text) Org-mode
file; the HTML file is created from this Org file (using org-mode allows
us to easily export the text in various formats). Those of you who want
to convert without ever opening emacs can run the command
 emacs --batch --eval '(and (find-file "codingstyle.org")
(org-export-as-html nil))'
from the command line.

Looking forward to your comments, both on this e-mail and the coding
standards.


Lennart.

On 02-05-13 15:15, Yurii Aulchenko wrote:
> Dear All,
> 
> I have recently received several requests from people who would like to
> join to the GenABEL project with their software. Given this is a
> community-based project, neither me nor someone else is in a position to
> say 'yes' or 'no' - we need to develop some procedure how a software
> joins the project. 
> 
> We have discussed this with Nicola and Lennart during EMGM-2013, and we
> think that we do need a technical review as a part of the procedure
> (addressing the issues of license, clarity of the code, integration with
> other packages, etc.). We also need to think how we do maintenance: the
> suggestion would be to request that the author joins the forum and the
> list. If we see that a package is not actively maintained (e.g. we can
> not reach the maintainer), we should tag such a package as 'orphaned'. 
> 
> In many respects, we can base our procedure on the procedures developed
> by Bioconductor. In our procedures we need to achieve two conflicting
> goals: a) we do not want to repel potential contributors by a long list
> of technical requirements but at the same time b) in the sake of
> maintainability we need the code to comply to some requirements.
> Probably we should have 'minimal' and 'complete' requirements with
> packages clearly tagged on the web pages.
> 
> Let us know what you think. I will initiate a PiratPad document after
> having initial response from you. 
> 
> best regards,
> YA
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
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From lennart at karssen.org  Tue May 14 19:13:24 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Tue, 14 May 2013 19:13:24 +0200
Subject: [GenABEL-dev] patch for bug #2525
In-Reply-To: <CAHX9t6+2LY-4PqXb6ocdB3YGWy=+eyEcHBdGk+h=AC74vPcOiQ@mail.gmail.com>
References: <E54DB40280C54723A3A0ACCBA7BEFE57@gmail.com>
 <CAHX9t6+2LY-4PqXb6ocdB3YGWy=+eyEcHBdGk+h=AC74vPcOiQ@mail.gmail.com>
Message-ID: <519270B4.7030708@karssen.org>

Dear Yurii,

I just tested export.plink() in the development version of GenABEL (SVN
r1214) to see if it still leaks memory, so bug 2055 isn't fixed by
Vladimir's fix, unfortunately.

FYI, to check this I ran:
library(GenABEL)
data(srdta)
export.plink(data=srdta, filebasename="plink", transpose=FALSE)

If you repeat the last statements a couple of times you'll see R's
memory use increase and only decrease when you exit R.

No idea about a unittest for this... Valgrind should be able to track
it. I'll have to read up on using Valgrind with C code in R...


Best,

Lennart.

On 04-04-13 13:44, Yurii Aulchenko wrote:
> Thank you, Vladimir! - nice fix! 
> 
> Lennart, I wonder if this fix somehow also address the export.plink bug
> #2055 discussed earlier. I also wonder what kind of unit test one can
> introduce for such 'memory leak' problem...
> 
> Below please find description of testing of the patch and some minor
> changes I introduced. I have updated the code on SVN
> (http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000575.html)
> and closed the bug. 
> 
> best wishes,
> Yurii
> 
> I have added a unit test for this bug in r. 1185,
> see http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000574.html)
> 
> Then I ran unit tests without applying the patch yet by 
> 
> cd pkg/GenABEL/inst/unitTests
> make
> 
> which gave me - as expected - 
> 
> GenABEL unit testing - 20 test functions, 1 error, 2 failures
> FAILURE in test.export.merlin.bug2525: Error in checkIdentical(xN, xO) :
> FALSE 
> FAILURE in test.exports: Error in checkIdentical(xN, xO) : FALSE 
> ERROR in test.impute2databel: Error in .Call("iterator",
> 
> (you can also check report.html for details; the FAILURE's are related
> to the bug 2525, and the ERROR is related to other bug, so our aim is to
> eliminate these FAILURES)
> 
> Next (from ../../../) I have applied the patch by 
> 
> patch -p0 -i ~/Downloads/patch_2525
> 
> and run unit tests again by
> 
> cd pkg/GenABEL/inst/unitTests
> make
> 
> which gave me 
> 
> GenABEL unit testing - 20 test functions, 1 error, 0 failures
> ERROR in test.impute2databel: Error in .Call("iterator",
> 
> which I thought was good - basically the test FAILURES were eliminated.
> 
> Now, the patch as submitted prints out much debugging (?) related staff
> to STDOUT, so next I commented out Rprintf's and ran the tests agin,
> getting 
> 
> GenABEL unit testing - 20 test functions, 1 error, 0 failures
> ERROR in test.impute2databel: Error in .Call("iterator", 
> 
> So, I conclude that the bug is fixed!
> 
> 
> On Wed, Apr 3, 2013 at 4:54 PM, Vladimir Naumov <looongdog at gmail.com
> <mailto:looongdog at gmail.com>> wrote:
> 
>     http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2525&group_id=505&atid=2058
> 
> 
>     It was problem with cycle that didn't renew sex values - so they
>     were periodically written into output file with period of 100 (by
>     default) 
> 
>     -- 
>     Vladimir Naumov
>     0079156727733
>     Skype: snow_wow
> 
> 
>     _______________________________________________
>     genabel-devel mailing list
>     genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> <http://twitter.com/YuriiAulchenko> ] [ Blog
> <http://yurii-aulchenko.blogspot.nl/> ]
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Wed May 15 12:28:15 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 15 May 2013 12:28:15 +0200
Subject: [GenABEL-dev] patch for bug #2525
In-Reply-To: <519270B4.7030708@karssen.org>
References: <E54DB40280C54723A3A0ACCBA7BEFE57@gmail.com>
 <CAHX9t6+2LY-4PqXb6ocdB3YGWy=+eyEcHBdGk+h=AC74vPcOiQ@mail.gmail.com>
 <519270B4.7030708@karssen.org>
Message-ID: <-2540231210239354973@unknownmsgid>

Pity. Thanks for the hint!

----------------------
Yurii Aulchenko
(sent from mobile device)

On 14 May 2013, at 19:13, "L.C. Karssen" <lennart at karssen.org> wrote:

> Dear Yurii,
>
> I just tested export.plink() in the development version of GenABEL (SVN
> r1214) to see if it still leaks memory, so bug 2055 isn't fixed by
> Vladimir's fix, unfortunately.
>
> FYI, to check this I ran:
> library(GenABEL)
> data(srdta)
> export.plink(data=srdta, filebasename="plink", transpose=FALSE)
>
> If you repeat the last statements a couple of times you'll see R's
> memory use increase and only decrease when you exit R.
>
> No idea about a unittest for this... Valgrind should be able to track
> it. I'll have to read up on using Valgrind with C code in R...
>
>
> Best,
>
> Lennart.
>
> On 04-04-13 13:44, Yurii Aulchenko wrote:
>> Thank you, Vladimir! - nice fix!
>>
>> Lennart, I wonder if this fix somehow also address the export.plink bug
>> #2055 discussed earlier. I also wonder what kind of unit test one can
>> introduce for such 'memory leak' problem...
>>
>> Below please find description of testing of the patch and some minor
>> changes I introduced. I have updated the code on SVN
>> (http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000575.html)
>> and closed the bug.
>>
>> best wishes,
>> Yurii
>>
>> I have added a unit test for this bug in r. 1185,
>> see http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000574.html)
>>
>> Then I ran unit tests without applying the patch yet by
>>
>> cd pkg/GenABEL/inst/unitTests
>> make
>>
>> which gave me - as expected -
>>
>> GenABEL unit testing - 20 test functions, 1 error, 2 failures
>> FAILURE in test.export.merlin.bug2525: Error in checkIdentical(xN, xO) :
>> FALSE
>> FAILURE in test.exports: Error in checkIdentical(xN, xO) : FALSE
>> ERROR in test.impute2databel: Error in .Call("iterator",
>>
>> (you can also check report.html for details; the FAILURE's are related
>> to the bug 2525, and the ERROR is related to other bug, so our aim is to
>> eliminate these FAILURES)
>>
>> Next (from ../../../) I have applied the patch by
>>
>> patch -p0 -i ~/Downloads/patch_2525
>>
>> and run unit tests again by
>>
>> cd pkg/GenABEL/inst/unitTests
>> make
>>
>> which gave me
>>
>> GenABEL unit testing - 20 test functions, 1 error, 0 failures
>> ERROR in test.impute2databel: Error in .Call("iterator",
>>
>> which I thought was good - basically the test FAILURES were eliminated.
>>
>> Now, the patch as submitted prints out much debugging (?) related staff
>> to STDOUT, so next I commented out Rprintf's and ran the tests agin,
>> getting
>>
>> GenABEL unit testing - 20 test functions, 1 error, 0 failures
>> ERROR in test.impute2databel: Error in .Call("iterator",
>>
>> So, I conclude that the bug is fixed!
>>
>>
>> On Wed, Apr 3, 2013 at 4:54 PM, Vladimir Naumov <looongdog at gmail.com
>> <mailto:looongdog at gmail.com>> wrote:
>>
>>    http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2525&group_id=505&atid=2058
>>
>>
>>    It was problem with cycle that didn't renew sex values - so they
>>    were periodically written into output file with period of 100 (by
>>    default)
>>
>>    --
>>    Vladimir Naumov
>>    0079156727733
>>    Skype: snow_wow
>>
>>
>>    _______________________________________________
>>    genabel-devel mailing list
>>    genabel-devel at lists.r-forge.r-project.org
>>    <mailto:genabel-devel at lists.r-forge.r-project.org>
>>    https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>>
>>
>>
>> --
>> -----------------------------------------------------
>> Yurii S. Aulchenko
>>
>> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
>> <http://twitter.com/YuriiAulchenko> ] [ Blog
>> <http://yurii-aulchenko.blogspot.nl/> ]
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

From yurii.aulchenko at gmail.com  Wed May 15 19:25:43 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 15 May 2013 19:25:43 +0200
Subject: [GenABEL-dev] [Genabel-commits] r1216 - www
In-Reply-To: <20130513224623.62767185378@r-forge.r-project.org>
References: <20130513224623.62767185378@r-forge.r-project.org>
Message-ID: <CAHX9t6KpD-GGebzkK5TD+katGTbTjbYLPeNS5FH7=9S5TQFoqg@mail.gmail.com>

Ha! Thanks fir this, Lennart!

I remember I added some comments on piratpad about Eclipse, but apparently
theu did not make it to the final document :)

YA

On Tue, May 14, 2013 at 12:46 AM, <noreply at r-forge.r-project.org> wrote:

> Author: lckarssen
> Date: 2013-05-14 00:46:23 +0200 (Tue, 14 May 2013)
> New Revision: 1216
>
> Modified:
>    www/index.php
> Log:
> Added a link to the coding style HTML page in the www folder to index.php.
>
>
> Modified: www/index.php
> ===================================================================
> --- www/index.php       2013-05-13 22:06:54 UTC (rev 1215)
> +++ www/index.php       2013-05-13 22:46:23 UTC (rev 1216)
> @@ -11,18 +11,18 @@
>  echo '<?xml version="1.0" encoding="UTF-8"?>';
>  ?>
>  <!DOCTYPE html
> -       PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
> -       "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
> +        PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
> +        "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
>  <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en   ">
>
>    <head>
> -       <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"
> />
> -       <title><?php echo $group_name; ?></title>
> -       <link href="<?php echo $themeroot; ?>styles/estilo1.css"
> rel="stylesheet" type="text/css" />
> -
> -
> -       <script type="text/javascript">
> +        <meta http-equiv="Content-Type" content="text/html;
> charset=UTF-8" />
> +        <title><?php echo $group_name; ?></title>
> +        <link href="<?php echo $themeroot; ?>styles/estilo1.css"
> rel="stylesheet" type="text/css" />
>
> +
> +        <script type="text/javascript">
> +
>    var _gaq = _gaq || [];
>    _gaq.push(['_setAccount', 'UA-12010288-7']);
>    _gaq.push(['_trackPageview']);
> @@ -34,8 +34,8 @@
>    })();
>
>  </script>
> -
> -
> +
> +
>    </head>
>
>  <body>
> @@ -53,7 +53,7 @@
>  <?php if ($handle=fopen('http://
> '.$domain.'/export/projtitl.php?group_name='.$group_name,'r')){
>  $contents = '';
>  while (!feof($handle)) {
> -       $contents .= fread($handle, 8192);
> +        $contents .= fread($handle, 8192);
>  }
>  fclose($handle);
>  echo $contents; } ?>
> @@ -63,7 +63,7 @@
>  <p>
>  <H3>
>  These R GenABEL's contributors' pages. The main web-site of GenABEL
> project is at <a href="http://www.genabel.org">www.GenABEL.org</a>
> -</H3>
> +</H3>
>  </p>
>
>  <p></p>
> @@ -72,6 +72,11 @@
>  </p>
>  <ul>
>  <li>
> +<a href="codingstyle.html">
> +The GenABEL project coding standards
> +</a>
> +</li>
> +<li>
>  <a href="tutHowToInstallDevelVersion.html">
>  How to install devel-version of GenABEL suite
>  </a> (for advanced users)
> @@ -88,14 +93,14 @@
>  </li>
>  <li>
>  <a href="tutHowToMakeTags.html">
> -How to tag released versions of GenABEL-suite packages
> +How to tag released versions of GenABEL-suite packages
>  </a>
>  </li>
>  </ul>
>
> -<p>
> -The <strong>project RForge pages</strong> you can find
> -<a href="http://<?php echo $domain; ?>/projects/<?php echo $group_name;
> ?>/"><strong>here</strong></a>.
> +<p>
> +The <strong>project RForge pages</strong> you can find
> +<a href="http://<?php echo $domain; ?>/projects/<?php echo $group_name;
> ?>/"><strong>here</strong></a>.
>  </p>
>
>  </body>
>
> _______________________________________________
> Genabel-commits mailing list
> Genabel-commits at lists.r-forge.r-project.org
>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From lennart at karssen.org  Fri May 17 09:28:48 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 17 May 2013 09:28:48 +0200
Subject: [GenABEL-dev] [Genabel-commits] r1216 - www
In-Reply-To: <CAHX9t6KpD-GGebzkK5TD+katGTbTjbYLPeNS5FH7=9S5TQFoqg@mail.gmail.com>
References: <20130513224623.62767185378@r-forge.r-project.org>
 <CAHX9t6KpD-GGebzkK5TD+katGTbTjbYLPeNS5FH7=9S5TQFoqg@mail.gmail.com>
Message-ID: <5195DC30.6020903@karssen.org>

Hi Yurii,

I hadn't seen your comments/changes to the piratepad document, so thanks
for bringing it up. I've imported them into the org file in SVN r1223.


Best,

Lennart.

On 15-05-13 19:25, Yurii Aulchenko wrote:
> Ha! Thanks fir this, Lennart!
> 
> I remember I added some comments on piratpad about Eclipse, but
> apparently theu did not make it to the final document :)
> 
> YA
> 
> On Tue, May 14, 2013 at 12:46 AM, <noreply at r-forge.r-project.org
> <mailto:noreply at r-forge.r-project.org>> wrote:
> 
>     Author: lckarssen
>     Date: 2013-05-14 00:46:23 +0200 (Tue, 14 May 2013)
>     New Revision: 1216
> 
>     Modified:
>        www/index.php
>     Log:
>     Added a link to the coding style HTML page in the www folder to
>     index.php.
> 
> 
>     Modified: www/index.php
>     ===================================================================
>     --- www/index.php       2013-05-13 22:06:54 UTC (rev 1215)
>     +++ www/index.php       2013-05-13 22:46:23 UTC (rev 1216)
>     @@ -11,18 +11,18 @@
>      echo '<?xml version="1.0" encoding="UTF-8"?>';
>      ?>
>      <!DOCTYPE html
>     -       PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
>     -       "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
>     +        PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
>     +        "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
>      <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en   ">
> 
>        <head>
>     -       <meta http-equiv="Content-Type" content="text/html; />
>     -       <title><?php echo $group_name; ?></title>
>     -       <link href="<?php echo $themeroot; ?>styles/estilo1.css"
>     rel="stylesheet" type="text/css" />
>     -
>     -
>     -       <script type="text/javascript">
>     +        <meta http-equiv="Content-Type" content="text/html;
>     charset=UTF-8" />
>     +        <title><?php echo $group_name; ?></title>
>     +        <link href="<?php echo $themeroot; ?>styles/estilo1.css"
>     rel="stylesheet" type="text/css" />
> 
>     +
>     +        <script type="text/javascript">
>     +
>        var _gaq = _gaq || [];
>        _gaq.push(['_setAccount', 'UA-12010288-7']);
>        _gaq.push(['_trackPageview']);
>     @@ -34,8 +34,8 @@
>        })();
> 
>      </script>
>     -
>     -
>     +
>     +
>        </head>
> 
>      <body>
>     @@ -53,7 +53,7 @@
>      <?php if
>     ($handle=fopen('http://'.$domain.'/export/projtitl.php?group_name='.$group_name,'r')){
>      $contents = '';
>      while (!feof($handle)) {
>     -       $contents .= fread($handle, 8192);
>     +        $contents .= fread($handle, 8192);
>      }
>      fclose($handle);
>      echo $contents; } ?>
>     @@ -63,7 +63,7 @@
>      <p>
>      <H3>
>      These R GenABEL's contributors' pages. The main web-site of GenABEL
>     project is at <a href="http://www.genabel.org">www.GenABEL.org
>     <http://www.GenABEL.org></a>
>     -</H3>
>     +</H3>
>      </p>
> 
>      <p></p>
>     @@ -72,6 +72,11 @@
>      </p>
>      <ul>
>      <li>
>     +<a href="codingstyle.html">
>     +The GenABEL project coding standards
>     +</a>
>     +</li>
>     +<li>
>      <a href="tutHowToInstallDevelVersion.html">
>      How to install devel-version of GenABEL suite
>      </a> (for advanced users)
>     @@ -88,14 +93,14 @@
>      </li>
>      <li>
>      <a href="tutHowToMakeTags.html">
>     -How to tag released versions of GenABEL-suite packages
>     +How to tag released versions of GenABEL-suite packages
>      </a>
>      </li>
>      </ul>
> 
>     -<p>
>     -The <strong>project RForge pages</strong> you can find
>     -<a href="http://<?php echo $domain; ?>/projects/<?php echo
>     $group_name; ?>/"><strong>here</strong></a>.
>     +<p>
>     +The <strong>project RForge pages</strong> you can find
>     +<a href="http://<?php echo $domain; ?>/projects/<?php echo
>     $group_name; ?>/"><strong>here</strong></a>.
>      </p>
> 
>      </body>
> 
>     _______________________________________________
>     Genabel-commits mailing list
>     Genabel-commits at lists.r-forge.r-project.org
>     <mailto:Genabel-commits at lists.r-forge.r-project.org>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> <http://twitter.com/YuriiAulchenko> ] [ Blog
> <http://yurii-aulchenko.blogspot.nl/> ]
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
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From nicola.pirastu at burlo.trieste.it  Wed May 22 09:55:39 2013
From: nicola.pirastu at burlo.trieste.it (Nicola Pirastu)
Date: Wed, 22 May 2013 09:55:39 +0200
Subject: [GenABEL-dev] joining the GenABEL project - what is the
	procedure?
In-Reply-To: <51916427.8020307@karssen.org>
References: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
 <51916427.8020307@karssen.org>
Message-ID: <CB4CF543-7387-4B98-B412-7ED794CEB37B@burlo.trieste.it>

Dear all,

I think that the best way we can discuss about this is to start with a real case. I would propose to start from the package
I've just written to run gene/region wide analysis which I've called RegionABEL.

It basically gives gene wide value with real or imputed data, with or without kinship included. It is not for analyzing rare variants, so it is not like SKAT. If you want to think of it in terms of existing software it is like VEGAS or plink-ave. The main advance is that since it does not use simulation/permutations to get pvalues it is much faster (4 hours on 1000G data vs 12-16 of VEGAS on HapMap 2.5). The other great advantage is that it does not require prior knowledge of LD as in other methods.
I have beta version of the package and I've written a Tutorial to explain how to use it.

So how do you think we should proceed now? Should we ask some volunteers to review it?


Best.

Nicola




Il giorno 14/mag/2013, alle ore 00:07, L.C. Karssen <lennart at karssen.org> ha scritto:

> Dear all,
>
> It's been a while but this mail was still on my todo list. I agree with
> Yurii that we should start establishing procedures for projects wanting
> to join the GenABEL project umbrella. Software lifecycle management is
> too often overlooked when developing a package and we don't want to
> 'degrade' the GenABEL project brand name by including packages that are
> not maintained anymore after the initial paper is published. Or, another
> argument I've come across: we make it open source so everyone can
> contribute to it (and therefore it will 'somehow' be maintained without
> us putting more effort into it). That's not how it works. The software
> ecosystem in which a package lives is dynamic and a package should adapt
> to that.
>
> As Yurii wrote we discussed this at the EMGM conference and agreed that
> code review should be part of it. This neatly ties into the discussion
> we had on thils list some time ago about coding standards. This does not
> mean we force everybody to use four spaces instead of eight when
> indenting code, but more serious stuff like variables named "a" or "df"
> are not helpful when someone wants to contribute or take over
> maintenance of the package.
>
> I've just committed the draft document of the coding standards to the
> www folder of the SVN repo (rev. 1215). It's a (plain text) Org-mode
> file; the HTML file is created from this Org file (using org-mode allows
> us to easily export the text in various formats). Those of you who want
> to convert without ever opening emacs can run the command
> emacs --batch --eval '(and (find-file "codingstyle.org")
> (org-export-as-html nil))'
> from the command line.
>
> Looking forward to your comments, both on this e-mail and the coding
> standards.
>
>
> Lennart.
>
> On 02-05-13 15:15, Yurii Aulchenko wrote:
>> Dear All,
>>
>> I have recently received several requests from people who would like to
>> join to the GenABEL project with their software. Given this is a
>> community-based project, neither me nor someone else is in a position to
>> say 'yes' or 'no' - we need to develop some procedure how a software
>> joins the project.
>>
>> We have discussed this with Nicola and Lennart during EMGM-2013, and we
>> think that we do need a technical review as a part of the procedure
>> (addressing the issues of license, clarity of the code, integration with
>> other packages, etc.). We also need to think how we do maintenance: the
>> suggestion would be to request that the author joins the forum and the
>> list. If we see that a package is not actively maintained (e.g. we can
>> not reach the maintainer), we should tag such a package as 'orphaned'.
>>
>> In many respects, we can base our procedure on the procedures developed
>> by Bioconductor. In our procedures we need to achieve two conflicting
>> goals: a) we do not want to repel potential contributors by a long list
>> of technical requirements but at the same time b) in the sake of
>> maintainability we need the code to comply to some requirements.
>> Probably we should have 'minimal' and 'complete' requirements with
>> packages clearly tagged on the web pages.
>>
>> Let us know what you think. I will initiate a PiratPad document after
>> having initial response from you.
>>
>> best regards,
>> YA
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you.

From lennart at karssen.org  Thu May 23 21:55:59 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 23 May 2013 21:55:59 +0200
Subject: [GenABEL-dev] Implementing p-value output in ProbABEL
Message-ID: <519E744F.7060601@karssen.org>

Dear list,

One of the long standing feature requests for ProbABEL (#2086 in the
tracker) has been adding p-values to the output files (at least for the
most-often used additive model based on dosage files).
Maarten and I have discussed this a while ago and we'd like to implement
this (Maarten actually already wrote a proof of principle).

Before we go for a certain implementation I'd like to start a discussion
on this list on how to deal with dependencies.
For this specific example we have the following options:
1) Implement p-value code ourselves (from scratch)
2) Use the R math library
3) Use the GNU Scientific Library
4) Use the Boost library

Option 1 is a bad one, because writing good code for extreme p-values is
not trivial and this problem has already been solved (by at least the
three other options in the list).

As to options 2-4 I'd like to hear your opinion on the following:
a) introducing dependencies on external libraries: with any of these
solutions we introduce a dependency for the people running ProbABEL.
Option 2 depends on R being present, 3 on the installation of the GSL
and option 3 on Boost. Note that (for efficient matrix math we already
recommend installing the Eigen headers, but that is only necessary when
compiling, not when running).
Personally I don't see this as a bad thing, especially since I can use
the ./configure mechanism to disable the feature if the lib is not installed
b) which lib would be best to use? Option 2 is easy (and we have
Maarten's p.o.p. code based on that). Option 3 would have been my first
choice and is also not difficult to program (also the GSL has been shown
to have a stable implementation for low p-values [1]). Option 3 is more
complex to program, but given the wide range of the Boost libs, we may
be able to leverage some of its other features as well (e.g.
reading/writing gzipped files).

So in short:
ad 2) easy, but large dependency on R (will probably also work on Windows)
ad 3) easy, simple, but may be more difficult for Windows (needs to be
checked)
ad 4) more difficult, but more possibilities for the future


Any thoughts/suggestions?

Thanks,

Lennart.
-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Sat May 25 15:20:02 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sat, 25 May 2013 20:20:02 +0700
Subject: [GenABEL-dev] Fwd: useR! 2013 abstract review notification
In-Reply-To: <56853BFE8EE95549AB5206735A3518DD3919E8@evsab04.uclm.es>
References: <56853BFE8EE95549AB5206735A3518DD3919E8@evsab04.uclm.es>
Message-ID: <CAHX9t6+B_H=ZFGWQc8KHrpdzqeKH5xweM7bC93-2FCMHaBsxMg@mail.gmail.com>

FYI

who else is going to UseR! conference?

Yurii

---------- Forwarded message ----------
From: useR2013 <congreso.user2013 at uclm.es>
Date: Wed, May 8, 2013 at 6:34 PM
Subject: useR! 2013 abstract review notification
To:


Dear colleague,****

We are pleased to inform you that your abstract has been accepted for being
presented at the useR! 2013 Conference as a contributed talk. As soon as
possible, the conference schedule will be available on the web site.****

** **

We remind that as in previous useR! conferences each registered participant
may just give one presentation (so a team of two people may give two
presentations if both persons are registered.)****

** **

** **

Thank you for submitting your proposal to the useR! 2013 Conference. ****

Best regards,****

Esteban Alfaro****

Noelia Garc?a****

On behalf of the Program Committee ****

** **



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From yurii.aulchenko at gmail.com  Sun May 26 09:22:26 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sun, 26 May 2013 14:22:26 +0700
Subject: [GenABEL-dev] Implementing p-value output in ProbABEL
In-Reply-To: <519E744F.7060601@karssen.org>
References: <519E744F.7060601@karssen.org>
Message-ID: <CAHX9t6LbP5ThP=Hy2ui9ON9Uq2OEGM35TPrHRMv4vmg5cun5bw@mail.gmail.com>

R: that may be too much to ask to install R as a 'library' :) however,
similarly to boost, this may provide with more opportunities in the future

GSL: to my experience should work across major platforms (at least I
remember compiling MixABEL for Win, and I am using MixABEL for Mac); using
GSL in MixABEL worked rather straightforwardly

boost: no experience

So I would personally be more inclined towards GSL, but only because I had
some experience with it. I have however heard that GSL is not-so-perfect
library ... so it may appear that eventually you want to switch to boost -
but for one function that should not be a big deal, right?

Thinking of the future, boost may indeed be the best option, but I
would definitely do some testing on different platforms. If you give me
clear instructions, I am willing to do testing for Mac.

Yurii

PS what is p.o.p. code?

On Fri, May 24, 2013 at 2:55 AM, L.C. Karssen <lennart at karssen.org> wrote:

> Dear list,
>
> One of the long standing feature requests for ProbABEL (#2086 in the
> tracker) has been adding p-values to the output files (at least for the
> most-often used additive model based on dosage files).
> Maarten and I have discussed this a while ago and we'd like to implement
> this (Maarten actually already wrote a proof of principle).
>
> Before we go for a certain implementation I'd like to start a discussion
> on this list on how to deal with dependencies.
> For this specific example we have the following options:
> 1) Implement p-value code ourselves (from scratch)
> 2) Use the R math library
> 3) Use the GNU Scientific Library
> 4) Use the Boost library
>
> Option 1 is a bad one, because writing good code for extreme p-values is
> not trivial and this problem has already been solved (by at least the
> three other options in the list).
>
> As to options 2-4 I'd like to hear your opinion on the following:
> a) introducing dependencies on external libraries: with any of these
> solutions we introduce a dependency for the people running ProbABEL.
> Option 2 depends on R being present, 3 on the installation of the GSL
> and option 3 on Boost. Note that (for efficient matrix math we already
> recommend installing the Eigen headers, but that is only necessary when
> compiling, not when running).
> Personally I don't see this as a bad thing, especially since I can use
> the ./configure mechanism to disable the feature if the lib is not
> installed
> b) which lib would be best to use? Option 2 is easy (and we have
> Maarten's p.o.p. code based on that). Option 3 would have been my first
> choice and is also not difficult to program (also the GSL has been shown
> to have a stable implementation for low p-values [1]). Option 3 is more
> complex to program, but given the wide range of the Boost libs, we may
> be able to leverage some of its other features as well (e.g.
> reading/writing gzipped files).
>
> So in short:
> ad 2) easy, but large dependency on R (will probably also work on Windows)
> ad 3) easy, simple, but may be more difficult for Windows (needs to be
> checked)
> ad 4) more difficult, but more possibilities for the future
>
>
> Any thoughts/suggestions?
>
> Thanks,
>
> Lennart.
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From yurii.aulchenko at gmail.com  Sun May 26 10:48:59 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sun, 26 May 2013 15:48:59 +0700
Subject: [GenABEL-dev] Fwd: Package GenABEL_1.7-6.tar.gz has been built for
	Windows
In-Reply-To: <01ce5312$Blat.v2.2.2$b93335ea@mail.statistik.tu-dortmund.de>
References: <01ce5312$Blat.v2.2.2$b93335ea@mail.statistik.tu-dortmund.de>
Message-ID: <CAHX9t6JVbpAOFbaPLBGENGB23RpiJUbHW6Yugb=tZ3GQ=_jN9A@mail.gmail.com>

FYI

Major changes cf previous CRAN release (1.7-4):

Thanks to Vladimir Naumov: Fixed bug [#2525]: sex coding is wrong when
exporting data with export.merlin(srdta[,1:2],dpieceFun="new")

Thanks to Lennart: Changed default behavior of the export.plink() version.
Export to .tped is now the default; warning message when user attempts to
produce .ped (see bug [#2055])

Thanks to Yurii: Fixed bug [#2672] (GenABEL::cocohet produces PNG graphics
by default, which prevented Mac OS build on CRAN in 1.7-4)

---------- Forwarded message ----------
From: <Uwe.Ligges at r-project.org>
Date: Fri, May 17, 2013 at 10:25 PM
Subject: Package GenABEL_1.7-6.tar.gz has been built for Windows
To: yurii at bionet.nsc.ru
Cc: Uwe.Ligges at r-project.org


Dear package maintainer,

this notification has been generated automatically.
Your package GenABEL_1.7-6.tar.gz has been built for Windows and
will be published within 24 hours in the corresponding CRAN directory.
R version 3.0.1 (2013-05-16)

All the best,
Uwe Ligges
(Maintainer of binary packages for Windows)




-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From lennart at karssen.org  Sun May 26 11:34:32 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Sun, 26 May 2013 11:34:32 +0200
Subject: [GenABEL-dev] Implementing p-value output in ProbABEL
In-Reply-To: <CAHX9t6LbP5ThP=Hy2ui9ON9Uq2OEGM35TPrHRMv4vmg5cun5bw@mail.gmail.com>
References: <519E744F.7060601@karssen.org>
 <CAHX9t6LbP5ThP=Hy2ui9ON9Uq2OEGM35TPrHRMv4vmg5cun5bw@mail.gmail.com>
Message-ID: <51A1D728.3090408@karssen.org>

Hi Yurii,

Thanks for your insights!

On 26-05-13 09:22, Yurii Aulchenko wrote:
> R: that may be too much to ask to install R as a 'library' :) however,
> similarly to boost, this may provide with more opportunities in the future
> 
> GSL: to my experience should work across major platforms (at least I
> remember compiling MixABEL for Win, and I am using MixABEL for Mac);
> using GSL in MixABEL worked rather straightforwardly

Good to hear that. I do find GSL's matrix/vector code a hassle to use.
> 
> boost: no experience
> 
> So I would personally be more inclined towards GSL, but only because I
> had some experience with it.

In fact, of all options I presented I also only have actual experience
(beyond a few simple tests) with the GSL.

> I have however heard that GSL is
> not-so-perfect library ... so it may appear that eventually you want to
> switch to boost - but for one function that should not be a big deal, right?

Probably not. Can you say something more about GSL being not so perfect?

> 
> Thinking of the future, boost may indeed be the best option, but I
> would definitely do some testing on different platforms. If you give me
> clear instructions, I am willing to do testing for Mac. 

Great!


> 
> Yurii
> 
> PS what is p.o.p. code?

Proof of principle.


Best,

Lennart.

> 
> On Fri, May 24, 2013 at 2:55 AM, L.C. Karssen <lennart at karssen.org
> <mailto:lennart at karssen.org>> wrote:
> 
>     Dear list,
> 
>     One of the long standing feature requests for ProbABEL (#2086 in the
>     tracker) has been adding p-values to the output files (at least for the
>     most-often used additive model based on dosage files).
>     Maarten and I have discussed this a while ago and we'd like to implement
>     this (Maarten actually already wrote a proof of principle).
> 
>     Before we go for a certain implementation I'd like to start a discussion
>     on this list on how to deal with dependencies.
>     For this specific example we have the following options:
>     1) Implement p-value code ourselves (from scratch)
>     2) Use the R math library
>     3) Use the GNU Scientific Library
>     4) Use the Boost library
> 
>     Option 1 is a bad one, because writing good code for extreme p-values is
>     not trivial and this problem has already been solved (by at least the
>     three other options in the list).
> 
>     As to options 2-4 I'd like to hear your opinion on the following:
>     a) introducing dependencies on external libraries: with any of these
>     solutions we introduce a dependency for the people running ProbABEL.
>     Option 2 depends on R being present, 3 on the installation of the GSL
>     and option 3 on Boost. Note that (for efficient matrix math we already
>     recommend installing the Eigen headers, but that is only necessary when
>     compiling, not when running).
>     Personally I don't see this as a bad thing, especially since I can use
>     the ./configure mechanism to disable the feature if the lib is not
>     installed
>     b) which lib would be best to use? Option 2 is easy (and we have
>     Maarten's p.o.p. code based on that). Option 3 would have been my first
>     choice and is also not difficult to program (also the GSL has been shown
>     to have a stable implementation for low p-values [1]). Option 3 is more
>     complex to program, but given the wide range of the Boost libs, we may
>     be able to leverage some of its other features as well (e.g.
>     reading/writing gzipped files).
> 
>     So in short:
>     ad 2) easy, but large dependency on R (will probably also work on
>     Windows)
>     ad 3) easy, simple, but may be more difficult for Windows (needs to be
>     checked)
>     ad 4) more difficult, but more possibilities for the future
> 
> 
>     Any thoughts/suggestions?
> 
>     Thanks,
> 
>     Lennart.
>     --
>     -----------------------------------------------------------------
>     L.C. Karssen
>     Utrecht
>     The Netherlands
> 
>     lennart at karssen.org <mailto:lennart at karssen.org>
>     http://blog.karssen.org
> 
>     Stuur mij aub geen Word of Powerpoint bestanden!
>     Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>     ------------------------------------------------------------------
> 
> 
>     _______________________________________________
>     genabel-devel mailing list
>     genabel-devel at lists.r-forge.r-project.org
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> <http://twitter.com/YuriiAulchenko> ] [ Blog
> <http://yurii-aulchenko.blogspot.nl/> ]

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Sun May 26 12:25:05 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sun, 26 May 2013 17:25:05 +0700
Subject: [GenABEL-dev] Implementing p-value output in ProbABEL
In-Reply-To: <51A1D728.3090408@karssen.org>
References: <519E744F.7060601@karssen.org>
 <CAHX9t6LbP5ThP=Hy2ui9ON9Uq2OEGM35TPrHRMv4vmg5cun5bw@mail.gmail.com>
 <51A1D728.3090408@karssen.org>
Message-ID: <CAHX9t6KMan_dqgXhhbzQZ4V7EVLR35JuatRfMgZ0k5q0EdbwPw@mail.gmail.com>

On Sun, May 26, 2013 at 4:34 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Hi Yurii,
>
> Thanks for your insights!
>
> On 26-05-13 09:22, Yurii Aulchenko wrote:
> > R: that may be too much to ask to install R as a 'library' :) however,
> > similarly to boost, this may provide with more opportunities in the
> future
> >
> > GSL: to my experience should work across major platforms (at least I
> > remember compiling MixABEL for Win, and I am using MixABEL for Mac);
> > using GSL in MixABEL worked rather straightforwardly
>
> Good to hear that. I do find GSL's matrix/vector code a hassle to use.
> >
> > boost: no experience
> >
> > So I would personally be more inclined towards GSL, but only because I
> > had some experience with it.
>
> In fact, of all options I presented I also only have actual experience
> (beyond a few simple tests) with the GSL.
>
> > I have however heard that GSL is
> > not-so-perfect library ... so it may appear that eventually you want to
> > switch to boost - but for one function that should not be a big deal,
> right?
>
> Probably not. Can you say something more about GSL being not so perfect?
>
>

Nothing specific to tell - just vaguely remember that someone was
commenting about GSL this way. May well be not true or true for some aspect
:)



> >
> > Thinking of the future, boost may indeed be the best option, but I
> > would definitely do some testing on different platforms. If you give me
> > clear instructions, I am willing to do testing for Mac.
>
> Great!
>
>
> >
> > Yurii
> >
> > PS what is p.o.p. code?
>
> Proof of principle.
>
>
> Best,
>
> Lennart.
>
> >
> > On Fri, May 24, 2013 at 2:55 AM, L.C. Karssen <lennart at karssen.org
> > <mailto:lennart at karssen.org>> wrote:
> >
> >     Dear list,
> >
> >     One of the long standing feature requests for ProbABEL (#2086 in the
> >     tracker) has been adding p-values to the output files (at least for
> the
> >     most-often used additive model based on dosage files).
> >     Maarten and I have discussed this a while ago and we'd like to
> implement
> >     this (Maarten actually already wrote a proof of principle).
> >
> >     Before we go for a certain implementation I'd like to start a
> discussion
> >     on this list on how to deal with dependencies.
> >     For this specific example we have the following options:
> >     1) Implement p-value code ourselves (from scratch)
> >     2) Use the R math library
> >     3) Use the GNU Scientific Library
> >     4) Use the Boost library
> >
> >     Option 1 is a bad one, because writing good code for extreme
> p-values is
> >     not trivial and this problem has already been solved (by at least the
> >     three other options in the list).
> >
> >     As to options 2-4 I'd like to hear your opinion on the following:
> >     a) introducing dependencies on external libraries: with any of these
> >     solutions we introduce a dependency for the people running ProbABEL.
> >     Option 2 depends on R being present, 3 on the installation of the GSL
> >     and option 3 on Boost. Note that (for efficient matrix math we
> already
> >     recommend installing the Eigen headers, but that is only necessary
> when
> >     compiling, not when running).
> >     Personally I don't see this as a bad thing, especially since I can
> use
> >     the ./configure mechanism to disable the feature if the lib is not
> >     installed
> >     b) which lib would be best to use? Option 2 is easy (and we have
> >     Maarten's p.o.p. code based on that). Option 3 would have been my
> first
> >     choice and is also not difficult to program (also the GSL has been
> shown
> >     to have a stable implementation for low p-values [1]). Option 3 is
> more
> >     complex to program, but given the wide range of the Boost libs, we
> may
> >     be able to leverage some of its other features as well (e.g.
> >     reading/writing gzipped files).
> >
> >     So in short:
> >     ad 2) easy, but large dependency on R (will probably also work on
> >     Windows)
> >     ad 3) easy, simple, but may be more difficult for Windows (needs to
> be
> >     checked)
> >     ad 4) more difficult, but more possibilities for the future
> >
> >
> >     Any thoughts/suggestions?
> >
> >     Thanks,
> >
> >     Lennart.
> >     --
> >     -----------------------------------------------------------------
> >     L.C. Karssen
> >     Utrecht
> >     The Netherlands
> >
> >     lennart at karssen.org <mailto:lennart at karssen.org>
> >     http://blog.karssen.org
> >
> >     Stuur mij aub geen Word of Powerpoint bestanden!
> >     Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> >     ------------------------------------------------------------------
> >
> >
> >     _______________________________________________
> >     genabel-devel mailing list
> >     genabel-devel at lists.r-forge.r-project.org
> >     <mailto:genabel-devel at lists.r-forge.r-project.org>
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >
> >
> >
> >
> > --
> > -----------------------------------------------------
> > Yurii S. Aulchenko
> >
> > [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> > <http://twitter.com/YuriiAulchenko> ] [ Blog
> > <http://yurii-aulchenko.blogspot.nl/> ]
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
>


-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From nicola.pirastu at burlo.trieste.it  Mon May 27 14:42:17 2013
From: nicola.pirastu at burlo.trieste.it (Nicola Pirastu)
Date: Mon, 27 May 2013 14:42:17 +0200
Subject: [GenABEL-dev] joining the GenABEL project - what is the
	procedure?
In-Reply-To: <51916427.8020307@karssen.org>
References: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
 <51916427.8020307@karssen.org>
Message-ID: <57E3C0F3-E615-483F-87DC-37A18A25B720@burlo.trieste.it>

Dear all,

since I was of the people who asked to submit a package to the project I have given some thoughts on the matter, I'll try to summarize them quickly and see what you think about it.

1) Types of contributions.

I think that people could have whole packages or single functions which they have developed and would like to contribute to the project. I don't think we should create a new *ABEL every new contribution we have but probably we should see if some of the existing packages could host the new functions. For example let's say the some one writes new metanalysis functions probably they should go under MetABEL instead of going under a new name. I think that as the project grows this will happen more and more often, so probably we should think about it before hand.

2) The review process.

I think that Yurii's idea of having a review process is very good since I think that we should give some type of guarantee of what goes under the *ABEL name.
I guess basic requirements should be that the method behind the new package has some scientific base and that it is correctly implemented.
For future maintenance the code should also be readable and commentated. I think it should also provide correct warnings about wrong object types and so on so that if it crushes people at least know what is going wrong.
We could also add a list of "strongly suggested" requirements like CRAN compatibility for R based packages.

3) Integrability across packages.

I think that one of the important points that makes the difference between the different softwares is how much things are easy to get done. I think that one thing we should strongly suggest is that the new packages are compatible with the old ones and that they integrate with them. For example it makes no sense to me to use other file formats that gwaa.data class for genotyped data and phenotypes while DatABEL format should be used for imputed data. I think that this should not be mandatory since we want to encourage people in using our platform for their methods but it should be one of the strongly suggested requirements.

4) Maintainance.

I think we should require people to keep their packages up to date. I don't think that we want people to just drop off they package, put the ABEL brand on it and then disappear into nothing. Contributors should also try to drop by the forum every once in a while to check that there are no unanswered questions about their package. I think that support is one of the things that make a difference in software usage.


Sorry for being long, but I guess that if we do this right from the beginning it will avoid problems.

Best

Nicola
AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you.

From yurii.aulchenko at gmail.com  Tue May 28 04:39:46 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 28 May 2013 09:39:46 +0700
Subject: [GenABEL-dev] joining the GenABEL project - what is the
	procedure?
In-Reply-To: <CB4CF543-7387-4B98-B412-7ED794CEB37B@burlo.trieste.it>
References: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
 <51916427.8020307@karssen.org>
 <CB4CF543-7387-4B98-B412-7ED794CEB37B@burlo.trieste.it>
Message-ID: <CAHX9t6+kfOPUCosuAaOhQsJLWdtef-cTmCH509fRrnj-fuNf7A@mail.gmail.com>

I think it may be indeed a good idea to start with a 'case' and
develop/tune the recommendations on the way. Nicola's new package would
provide a good starting point (then we actually can think of re-review of
some of the packages which are in the GenABEL suite already).

What about following plan

1) We (Nicola, Yurii, ...) draft reviewer's instructions (starting with
points made during this discussion) - I made a piratepad
http://piratepad.net/9ExdfmuJHV (at the moment simply a copy of latest
Nicola's email); later we will circulate the draft on the list

2) Take RegionABEL as an example (I am volunteering to be the 'test'
reviewer), and explore this case to check the review procedure. Nicola, may
be you can send me the code already.

3) Ask an external person to act as a reviewer - this is for testing our
reviewers' instructions

The whole process (esp if we want to go for (3)) may take a couple of
months. Nicola, how much in hurry are you with publication?

Yurii


On Wed, May 22, 2013 at 2:55 PM, Nicola Pirastu <
nicola.pirastu at burlo.trieste.it> wrote:

> Dear all,
>
> I think that the best way we can discuss about this is to start with a
> real case. I would propose to start from the package
> I've just written to run gene/region wide analysis which I've called
> RegionABEL.
>
> It basically gives gene wide value with real or imputed data, with or
> without kinship included. It is not for analyzing rare variants, so it is
> not like SKAT. If you want to think of it in terms of existing software it
> is like VEGAS or plink-ave. The main advance is that since it does not use
> simulation/permutations to get pvalues it is much faster (4 hours on 1000G
> data vs 12-16 of VEGAS on HapMap 2.5). The other great advantage is that it
> does not require prior knowledge of LD as in other methods.
> I have beta version of the package and I've written a Tutorial to explain
> how to use it.
>
> So how do you think we should proceed now? Should we ask some volunteers
> to review it?
>
>
> Best.
>
> Nicola
>
>
>
>
> Il giorno 14/mag/2013, alle ore 00:07, L.C. Karssen <lennart at karssen.org>
> ha scritto:
>
> > Dear all,
> >
> > It's been a while but this mail was still on my todo list. I agree with
> > Yurii that we should start establishing procedures for projects wanting
> > to join the GenABEL project umbrella. Software lifecycle management is
> > too often overlooked when developing a package and we don't want to
> > 'degrade' the GenABEL project brand name by including packages that are
> > not maintained anymore after the initial paper is published. Or, another
> > argument I've come across: we make it open source so everyone can
> > contribute to it (and therefore it will 'somehow' be maintained without
> > us putting more effort into it). That's not how it works. The software
> > ecosystem in which a package lives is dynamic and a package should adapt
> > to that.
> >
> > As Yurii wrote we discussed this at the EMGM conference and agreed that
> > code review should be part of it. This neatly ties into the discussion
> > we had on thils list some time ago about coding standards. This does not
> > mean we force everybody to use four spaces instead of eight when
> > indenting code, but more serious stuff like variables named "a" or "df"
> > are not helpful when someone wants to contribute or take over
> > maintenance of the package.
> >
> > I've just committed the draft document of the coding standards to the
> > www folder of the SVN repo (rev. 1215). It's a (plain text) Org-mode
> > file; the HTML file is created from this Org file (using org-mode allows
> > us to easily export the text in various formats). Those of you who want
> > to convert without ever opening emacs can run the command
> > emacs --batch --eval '(and (find-file "codingstyle.org")
> > (org-export-as-html nil))'
> > from the command line.
> >
> > Looking forward to your comments, both on this e-mail and the coding
> > standards.
> >
> >
> > Lennart.
> >
> > On 02-05-13 15:15, Yurii Aulchenko wrote:
> >> Dear All,
> >>
> >> I have recently received several requests from people who would like to
> >> join to the GenABEL project with their software. Given this is a
> >> community-based project, neither me nor someone else is in a position to
> >> say 'yes' or 'no' - we need to develop some procedure how a software
> >> joins the project.
> >>
> >> We have discussed this with Nicola and Lennart during EMGM-2013, and we
> >> think that we do need a technical review as a part of the procedure
> >> (addressing the issues of license, clarity of the code, integration with
> >> other packages, etc.). We also need to think how we do maintenance: the
> >> suggestion would be to request that the author joins the forum and the
> >> list. If we see that a package is not actively maintained (e.g. we can
> >> not reach the maintainer), we should tag such a package as 'orphaned'.
> >>
> >> In many respects, we can base our procedure on the procedures developed
> >> by Bioconductor. In our procedures we need to achieve two conflicting
> >> goals: a) we do not want to repel potential contributors by a long list
> >> of technical requirements but at the same time b) in the sake of
> >> maintainability we need the code to comply to some requirements.
> >> Probably we should have 'minimal' and 'complete' requirements with
> >> packages clearly tagged on the web pages.
> >>
> >> Let us know what you think. I will initiate a PiratPad document after
> >> having initial response from you.
> >>
> >> best regards,
> >> YA
> >>
> >>
> >> _______________________________________________
> >> genabel-devel mailing list
> >> genabel-devel at lists.r-forge.r-project.org
> >>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>
> >
> > --
> > -----------------------------------------------------------------
> > L.C. Karssen
> > Utrecht
> > The Netherlands
> >
> > lennart at karssen.org
> > http://blog.karssen.org
> >
> > Stuur mij aub geen Word of Powerpoint bestanden!
> > Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> > ------------------------------------------------------------------
> >
> > _______________________________________________
> > genabel-devel mailing list
> > genabel-devel at lists.r-forge.r-project.org
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
> AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel
> messaggio o nei suoi allegati. Se non siete i destinatari indicati nel
> messaggio, o responsabili per la sua consegna alla persona, o se avete
> ricevuto il messaggio per errore, siete pregati di non trascriverlo,
> copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il
> messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential
> information may be contained in this message or in its attachments. If you
> are not the addressee indicated in this message, or responsible for message
> delivering to that person, or if you have received this message in error,
> you may not transcribe, copy or deliver this message to anyone. In that
> case, you should delete this message and its attachments. Thank you.
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From nicola.pirastu at burlo.trieste.it  Tue May 28 08:52:39 2013
From: nicola.pirastu at burlo.trieste.it (Nicola Pirastu)
Date: Tue, 28 May 2013 08:52:39 +0200
Subject: [GenABEL-dev] joining the GenABEL project - what is the
	procedure?
In-Reply-To: <CAHX9t6+kfOPUCosuAaOhQsJLWdtef-cTmCH509fRrnj-fuNf7A@mail.gmail.com>
References: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
 <51916427.8020307@karssen.org>
 <CB4CF543-7387-4B98-B412-7ED794CEB37B@burlo.trieste.it>
 <CAHX9t6+kfOPUCosuAaOhQsJLWdtef-cTmCH509fRrnj-fuNf7A@mail.gmail.com>
Message-ID: <E6BAADB6-B7B5-4DBF-BB6C-BED1013740AD@burlo.trieste.it>

Hi,

I think this is a very good plan. As for time I think a couple of months is fine, I still need to do some work to demonstrate that everything works fine (simulations, etc etc?.). Actually if some one would like to lend a hand on that side he/she would be more than welcome :).

I'll send you the code separately with a tutorial attached so we can get started.

Best.

Nicola


Il giorno 28/mag/2013, alle ore 04:39, Yurii Aulchenko <yurii.aulchenko at gmail.com<mailto:yurii.aulchenko at gmail.com>> ha scritto:

I think it may be indeed a good idea to start with a 'case' and develop/tune the recommendations on the way. Nicola's new package would provide a good starting point (then we actually can think of re-review of some of the packages which are in the GenABEL suite already).

What about following plan

1) We (Nicola, Yurii, ...) draft reviewer's instructions (starting with points made during this discussion) - I made a piratepad http://piratepad.net/9ExdfmuJHV (at the moment simply a copy of latest Nicola's email); later we will circulate the draft on the list

2) Take RegionABEL as an example (I am volunteering to be the 'test' reviewer), and explore this case to check the review procedure. Nicola, may be you can send me the code already.

3) Ask an external person to act as a reviewer - this is for testing our reviewers' instructions

The whole process (esp if we want to go for (3)) may take a couple of months. Nicola, how much in hurry are you with publication?

Yurii


On Wed, May 22, 2013 at 2:55 PM, Nicola Pirastu <nicola.pirastu at burlo.trieste.it<mailto:nicola.pirastu at burlo.trieste.it>> wrote:
Dear all,

I think that the best way we can discuss about this is to start with a real case. I would propose to start from the package
I've just written to run gene/region wide analysis which I've called RegionABEL.

It basically gives gene wide value with real or imputed data, with or without kinship included. It is not for analyzing rare variants, so it is not like SKAT. If you want to think of it in terms of existing software it is like VEGAS or plink-ave. The main advance is that since it does not use simulation/permutations to get pvalues it is much faster (4 hours on 1000G data vs 12-16 of VEGAS on HapMap 2.5). The other great advantage is that it does not require prior knowledge of LD as in other methods.
I have beta version of the package and I've written a Tutorial to explain how to use it.

So how do you think we should proceed now? Should we ask some volunteers to review it?


Best.

Nicola




Il giorno 14/mag/2013, alle ore 00:07, L.C. Karssen <lennart at karssen.org<mailto:lennart at karssen.org>> ha scritto:

> Dear all,
>
> It's been a while but this mail was still on my todo list. I agree with
> Yurii that we should start establishing procedures for projects wanting
> to join the GenABEL project umbrella. Software lifecycle management is
> too often overlooked when developing a package and we don't want to
> 'degrade' the GenABEL project brand name by including packages that are
> not maintained anymore after the initial paper is published. Or, another
> argument I've come across: we make it open source so everyone can
> contribute to it (and therefore it will 'somehow' be maintained without
> us putting more effort into it). That's not how it works. The software
> ecosystem in which a package lives is dynamic and a package should adapt
> to that.
>
> As Yurii wrote we discussed this at the EMGM conference and agreed that
> code review should be part of it. This neatly ties into the discussion
> we had on thils list some time ago about coding standards. This does not
> mean we force everybody to use four spaces instead of eight when
> indenting code, but more serious stuff like variables named "a" or "df"
> are not helpful when someone wants to contribute or take over
> maintenance of the package.
>
> I've just committed the draft document of the coding standards to the
> www folder of the SVN repo (rev. 1215). It's a (plain text) Org-mode
> file; the HTML file is created from this Org file (using org-mode allows
> us to easily export the text in various formats). Those of you who want
> to convert without ever opening emacs can run the command
> emacs --batch --eval '(and (find-file "codingstyle.org<http://codingstyle.org/>")
> (org-export-as-html nil))'
> from the command line.
>
> Looking forward to your comments, both on this e-mail and the coding
> standards.
>
>
> Lennart.
>
> On 02-05-13 15:15, Yurii Aulchenko wrote:
>> Dear All,
>>
>> I have recently received several requests from people who would like to
>> join to the GenABEL project with their software. Given this is a
>> community-based project, neither me nor someone else is in a position to
>> say 'yes' or 'no' - we need to develop some procedure how a software
>> joins the project.
>>
>> We have discussed this with Nicola and Lennart during EMGM-2013, and we
>> think that we do need a technical review as a part of the procedure
>> (addressing the issues of license, clarity of the code, integration with
>> other packages, etc.). We also need to think how we do maintenance: the
>> suggestion would be to request that the author joins the forum and the
>> list. If we see that a package is not actively maintained (e.g. we can
>> not reach the maintainer), we should tag such a package as 'orphaned'.
>>
>> In many respects, we can base our procedure on the procedures developed
>> by Bioconductor. In our procedures we need to achieve two conflicting
>> goals: a) we do not want to repel potential contributors by a long list
>> of technical requirements but at the same time b) in the sake of
>> maintainability we need the code to comply to some requirements.
>> Probably we should have 'minimal' and 'complete' requirements with
>> packages clearly tagged on the web pages.
>>
>> Let us know what you think. I will initiate a PiratPad document after
>> having initial response from you.
>>
>> best regards,
>> YA
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org<mailto:lennart at karssen.org>
> http://blog.karssen.org<http://blog.karssen.org/>
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you.
_______________________________________________
genabel-devel mailing list
genabel-devel at lists.r-forge.r-project.org<mailto:genabel-devel at lists.r-forge.r-project.org>
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel



--
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn<http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter<http://twitter.com/YuriiAulchenko> ] [ Blog<http://yurii-aulchenko.blogspot.nl/> ]

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From yurii.aulchenko at gmail.com  Tue May 28 13:25:10 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 28 May 2013 18:25:10 +0700
Subject: [GenABEL-dev] joining the GenABEL project - what is the
	procedure?
In-Reply-To: <E6BAADB6-B7B5-4DBF-BB6C-BED1013740AD@burlo.trieste.it>
References: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
 <51916427.8020307@karssen.org>
 <CB4CF543-7387-4B98-B412-7ED794CEB37B@burlo.trieste.it>
 <CAHX9t6+kfOPUCosuAaOhQsJLWdtef-cTmCH509fRrnj-fuNf7A@mail.gmail.com>
 <E6BAADB6-B7B5-4DBF-BB6C-BED1013740AD@burlo.trieste.it>
Message-ID: <CAHX9t6JV5JbjnHMS3WyHpS8mFip4R1QiwJGaYyxXXrT9Xyb9vg@mail.gmail.com>

Great, thank you, Nicola,

I think we should aim to have instructions and internal review finished in
1 mo, and then ask someone (external friends?) to do another review within
the next month

Yurii

On Tue, May 28, 2013 at 1:52 PM, Nicola Pirastu <
nicola.pirastu at burlo.trieste.it> wrote:

>  Hi,
>
>  I think this is a very good plan. As for time I think a couple of months
> is fine, I still need to do some work to demonstrate that everything works
> fine (simulations, etc etc?.). Actually if some one would like to lend a
> hand on that side he/she would be more than welcome :).
>
>  I'll send you the code separately with a tutorial attached so we can get
> started.
>
>  Best.
>
>  Nicola
>
>
>  Il giorno 28/mag/2013, alle ore 04:39, Yurii Aulchenko <
> yurii.aulchenko at gmail.com> ha scritto:
>
> I think it may be indeed a good idea to start with a 'case' and
> develop/tune the recommendations on the way. Nicola's new package would
> provide a good starting point (then we actually can think of re-review of
> some of the packages which are in the GenABEL suite already).
>
>  What about following plan
>
>  1) We (Nicola, Yurii, ...) draft reviewer's instructions (starting with
> points made during this discussion) - I made a piratepad
> http://piratepad.net/9ExdfmuJHV (at the moment simply a copy of latest
> Nicola's email); later we will circulate the draft on the list
>
>  2) Take RegionABEL as an example (I am volunteering to be the 'test'
> reviewer), and explore this case to check the review procedure. Nicola, may
> be you can send me the code already.
>
>  3) Ask an external person to act as a reviewer - this is for testing our
> reviewers' instructions
>
>  The whole process (esp if we want to go for (3)) may take a couple of
> months. Nicola, how much in hurry are you with publication?
>
>  Yurii
>
>
> On Wed, May 22, 2013 at 2:55 PM, Nicola Pirastu <
> nicola.pirastu at burlo.trieste.it> wrote:
>
>> Dear all,
>>
>> I think that the best way we can discuss about this is to start with a
>> real case. I would propose to start from the package
>> I've just written to run gene/region wide analysis which I've called
>> RegionABEL.
>>
>> It basically gives gene wide value with real or imputed data, with or
>> without kinship included. It is not for analyzing rare variants, so it is
>> not like SKAT. If you want to think of it in terms of existing software it
>> is like VEGAS or plink-ave. The main advance is that since it does not use
>> simulation/permutations to get pvalues it is much faster (4 hours on 1000G
>> data vs 12-16 of VEGAS on HapMap 2.5). The other great advantage is that it
>> does not require prior knowledge of LD as in other methods.
>> I have beta version of the package and I've written a Tutorial to explain
>> how to use it.
>>
>> So how do you think we should proceed now? Should we ask some volunteers
>> to review it?
>>
>>
>> Best.
>>
>> Nicola
>>
>>
>>
>>
>> Il giorno 14/mag/2013, alle ore 00:07, L.C. Karssen <lennart at karssen.org>
>> ha scritto:
>>
>> > Dear all,
>> >
>> > It's been a while but this mail was still on my todo list. I agree with
>> > Yurii that we should start establishing procedures for projects wanting
>> > to join the GenABEL project umbrella. Software lifecycle management is
>> > too often overlooked when developing a package and we don't want to
>> > 'degrade' the GenABEL project brand name by including packages that are
>> > not maintained anymore after the initial paper is published. Or, another
>> > argument I've come across: we make it open source so everyone can
>> > contribute to it (and therefore it will 'somehow' be maintained without
>> > us putting more effort into it). That's not how it works. The software
>> > ecosystem in which a package lives is dynamic and a package should adapt
>> > to that.
>> >
>> > As Yurii wrote we discussed this at the EMGM conference and agreed that
>> > code review should be part of it. This neatly ties into the discussion
>> > we had on thils list some time ago about coding standards. This does not
>> > mean we force everybody to use four spaces instead of eight when
>> > indenting code, but more serious stuff like variables named "a" or "df"
>> > are not helpful when someone wants to contribute or take over
>> > maintenance of the package.
>> >
>> > I've just committed the draft document of the coding standards to the
>> > www folder of the SVN repo (rev. 1215). It's a (plain text) Org-mode
>> > file; the HTML file is created from this Org file (using org-mode allows
>> > us to easily export the text in various formats). Those of you who want
>> > to convert without ever opening emacs can run the command
>> > emacs --batch --eval '(and (find-file "codingstyle.org")
>> > (org-export-as-html nil))'
>> > from the command line.
>> >
>> > Looking forward to your comments, both on this e-mail and the coding
>> > standards.
>> >
>> >
>> > Lennart.
>> >
>> > On 02-05-13 15:15, Yurii Aulchenko wrote:
>> >> Dear All,
>> >>
>> >> I have recently received several requests from people who would like to
>> >> join to the GenABEL project with their software. Given this is a
>> >> community-based project, neither me nor someone else is in a position
>> to
>> >> say 'yes' or 'no' - we need to develop some procedure how a software
>> >> joins the project.
>> >>
>> >> We have discussed this with Nicola and Lennart during EMGM-2013, and we
>> >> think that we do need a technical review as a part of the procedure
>> >> (addressing the issues of license, clarity of the code, integration
>> with
>> >> other packages, etc.). We also need to think how we do maintenance: the
>> >> suggestion would be to request that the author joins the forum and the
>> >> list. If we see that a package is not actively maintained (e.g. we can
>> >> not reach the maintainer), we should tag such a package as 'orphaned'.
>> >>
>> >> In many respects, we can base our procedure on the procedures developed
>> >> by Bioconductor. In our procedures we need to achieve two conflicting
>> >> goals: a) we do not want to repel potential contributors by a long list
>> >> of technical requirements but at the same time b) in the sake of
>> >> maintainability we need the code to comply to some requirements.
>> >> Probably we should have 'minimal' and 'complete' requirements with
>> >> packages clearly tagged on the web pages.
>> >>
>> >> Let us know what you think. I will initiate a PiratPad document after
>> >> having initial response from you.
>> >>
>> >> best regards,
>> >> YA
>> >>
>> >>
>> >> _______________________________________________
>> >> genabel-devel mailing list
>> >> genabel-devel at lists.r-forge.r-project.org
>> >>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>
>> >
>> > --
>> > -----------------------------------------------------------------
>> > L.C. Karssen
>> > Utrecht
>> > The Netherlands
>> >
>> > lennart at karssen.org
>> > http://blog.karssen.org
>> >
>> > Stuur mij aub geen Word of Powerpoint bestanden!
>> > Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>> > ------------------------------------------------------------------
>> >
>> > _______________________________________________
>> > genabel-devel mailing list
>> > genabel-devel at lists.r-forge.r-project.org
>> >
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>>  AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute
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>> are not the addressee indicated in this message, or responsible for message
>> delivering to that person, or if you have received this message in error,
>> you may not transcribe, copy or deliver this message to anyone. In that
>> case, you should delete this message and its attachments. Thank you.
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>
>
>
>  --
> -----------------------------------------------------
> Yurii S. Aulchenko
>
>  [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter<http://twitter.com/YuriiAulchenko>] [
> Blog <http://yurii-aulchenko.blogspot.nl/> ]
>
>
>  AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute
> nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel
> messaggio, o responsabili per la sua consegna alla persona, o se avete
> ricevuto il messaggio per errore, siete pregati di non trascriverlo,
> copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il
> messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential
> information may be contained in this message or in its attachments. If you
> are not the addressee indicated in this message, or responsible for message
> delivering to that person, or if you have received this message in error,
> you may not transcribe, copy or deliver this message to anyone. In that
> case, you should delete this message and its attachments. Thank you.
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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